Methods and compositions for targeting rna polymerases and non-coding rna biogenesis to specific loci

ABSTRACT

The present disclosure relates to recombinant proteins that induce epigenetic gene silencing and to methods of using such proteins for reducing the expression of genes in plants.

CROSS-REFERENCE TO RELATED APPLICATION(S)

This application claims the benefit of U.S. Provisional Application No.61/771,743, filed Mar. 1, 2013, and U.S. Provisional Application No.61/929,414, filed Jan. 20, 2014, which are both hereby incorporatedherein by reference in their entirety.

STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH

This invention was made with government support under Grant No. GM60398,awarded by the National Institutes of Health. The government has certainrights in the invention.

SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE

The content of the following submission on ASCII text file isincorporated herein by reference in its entirety: a computer readableform (CRF) of the Sequence Listing (file name:262232000440SEQLISTING.txt, date recorded: Feb. 28, 2014, size: 712 KB).

FIELD

The present disclosure relates to recombinant proteins that induceepigenetic gene silencing and to methods of using such proteins forreducing the expression of genes in plants.

BACKGROUND

Epigenetic marks are enzyme-mediated chemical modifications of DNA andof its associated chromatin proteins. Although epigenetic marks do notalter the primary sequence of DNA, they do contain heritable informationand play key roles in regulating genome function. Such modifications,including cytosine methylation, posttranslational modifications ofhistone tails and the histone core, and the positioning of nucleosomes(histone octamers wrapped with DNA), influence the transcriptional stateand other functional aspects of chromatin. For example, methylation ofDNA and certain residues on the histone H3 N-terminal tail, such as H3lysine 9 (H3K9), are important for transcriptional gene silencing andthe formation of heterochromatin. Such marks are essential for thesilencing of nongenic sequences, including transposons, pseudogenes,repetitive sequences, and integrated viruses, that become deleterious tocells if expressed and hence activated. Epigenetic gene silencing isalso important in developmental phenomena such as imprinting in bothplants and mammals, as well as in cell differentiation andreprogramming.

Different pathways involved in epigenetic silencing have been previouslydescribed, and include histone deacetylation, H3K27 and H3K9methylation, H3K4 demethylation, and DNA methylation of promoters. Anavenue to achieve DNA methylation is via a phenomenon known asRNA-directed DNA methylation, where non-coding RNAs act to directmethylation of a DNA sequence. In plants, no proteins have beendescribed that link the recognition of a specific DNA sequence with theestablishment of an epigenetic state. Thus, plant epigenetic regulatorsgenerally cannot be used for epigenetic silencing of specific genes ortransgenes in plants.

One solution is to identify or engineer epigenetic regulators thatcontain sequence-specific zinc finger domains, since zinc fingers werefirst identified as DNA-binding motifs (Miller et al., 1985), andnumerous other variations of them have been characterized. Recentprogress has been made that allows the engineering of DNA-bindingproteins that specifically recognize any desired DNA sequence. Forexample, it was recently shown that a three-finger zinc finger proteincould be constructed to block the expression of a human oncogene thatwas transformed into a mouse cell line (Choo and Klug, 1994). However,potential problems to engineering epigenetic regulators that contain anengineered zinc finger domain include ensuring that the engineeredprotein will have the correct folding to be functional, and ensuringthat the fusion of the zinc finger domain to the epigenetic regulatordoes not interfere with either the DNA-specific binding of the zincfinger domain or the activity of the epigenetic regulator.

Accordingly, a need exists for improved epigenetic regulators that arecapable of binding specific DNA sequences, that fold properly, and thatretain both the sequence-specific DNA-binding activity and epigeneticgene silencing activity when expressed in plants.

BRIEF SUMMARY

The present disclosure relates to a method for reducing expression ofone or more target nucleic acids in a plant, including: a) providing aplant containing a recombinant nucleic acid, where the recombinantnucleic acid encodes a recombinant polypeptide including a first aminoacid sequence including a DNA-binding domain and a second amino acidsequence including an SHH1 polypeptide or a fragment thereof; and b)growing the plant under conditions where the recombinant polypeptideencoded by the recombinant nucleic acid is expressed and binds to theone or more target nucleic acids, thereby reducing expression of the oneor more target nucleic acids. In some embodiments, the DNA-bindingdomain includes a zinc finger domain. In some embodiments, the zincfinger domain includes two, three, four, five, six, seven, eight, ornine zinc fingers. In some embodiments, the zinc finger domain is a zincfinger array. In some embodiments, the zinc finger domain is selectedfrom a Cys2His2 (C2H2) zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain is selected from a TAL effectortargeting domain, a helix-turn-helix family DNA-binding domain, a basicdomain, a ribbon-helix-helix domain, a TBP domain, a barrel dimerdomain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes threeC2H2 zinc finger domains. In some embodiments that may be combined withany of the preceding embodiments, the second amino acid sequenceincludes at least one of a homeodomain or a SAWADEE domain. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that isat least 50%, at least 55%, at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identical to SEQ ID NO: 1. Insome embodiments that may be combined with any of the precedingembodiments, the second amino acid sequence includes an amino acidsequence that is 100% identical to SEQ ID NO: 1. In some embodimentsthat may be combined with any of the preceding embodiments, therecombinant polypeptide interacts with an RNA polymerase. In someembodiments, the RNA polymerase is RNA polymerase IV. In someembodiments that may be combined with any of the preceding embodiments,the recombinant polypeptide interacts with methylated H3K9. In someembodiments that may be combined with any of the preceding embodiments,the recombinant polypeptide interacts with H3K9me1, H3K9me2, and/orH3K9me3. In some embodiments that may be combined with any of thepreceding embodiments, the recombinant polypeptide induces RNA-directedDNA methylation. In some embodiments that may be combined with any ofthe preceding embodiments, the one or more target nucleic acids areendogenous nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the one or more target nucleicacids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding an SHH1-like protein containing a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding an SHH1 polypeptide or a fragment thereof. In someembodiments, the second amino acid sequence incudes an amino acidsequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75% at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 1. In some embodiments, the second amino acid sequence includesan amino acid sequence that is 100% identical to SEQ ID NO: 1. In someembodiments that may be combined with any of the preceding embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a C2H2 zinc finger domain, a CCCH zincfinger domain, a multi-cysteine zinc finger domain, and a zinc binuclearcluster domain. In some embodiments that may be combined with any of thepreceding embodiments, the DNA-binding domain is selected from a TALeffector targeting domain, a helix-turn-helix family DNA-binding domain,a basic domain, a ribbon-helix-helix domain, a TBP domain, a barreldimer domain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the SHH1-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, theSHH1-like protein silences expression of the one or more target nucleicacids.

Other aspects of the present disclosure relate to a vector containingthe recombinant nucleic acid encoding the SHH1-like protein of any ofthe preceding embodiments, where the recombinant nucleic acid isoperably linked to a regulatory sequence. Other aspects of the presentdisclosure relate to a host cell containing the expression vector of thepreceding embodiment. In certain embodiments, the host cell is a plantcell. Other aspects of the present disclosure relate to a recombinantplant containing the recombinant nucleic acid of any of the precedingembodiments.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including a SUVH2 polypeptide or a fragment thereof,or a SUVH9 polypeptide or a fragment thereof; and b) growing the plantunder conditions where the recombinant polypeptide encoded by therecombinant nucleic acid is expressed and binds to the one or moretarget nucleic acids, thereby reducing expression of the one or moretarget nucleic acids. In some embodiments, the DNA-binding domainincludes a zinc finger domain. In some embodiments, the zinc fingerdomain includes two, three, four, five, six, seven, eight, or nine zincfingers. In some embodiments, the zinc finger domain is a zinc fingerarray. In some embodiments, the zinc finger domain is selected from aCys2His2 (C2H2) zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain is selected from a TAL effectortargeting domain, a helix-turn-helix family DNA-binding domain, a basicdomain, a ribbon-helix-helix domain, a TBP domain, a barrel dimerdomain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes threeC2H2 zinc finger domains. In some embodiments that may be combined withany of the preceding embodiments, the second amino acid sequenceincludes a domain selected from a two-helix bundle domain, a SRA domain,a pre-SET domain, or a SET domain. In some embodiments that may becombined with any of the preceding embodiments, the second amino acidsequence includes an amino acid sequence that is at least 50%, at least55%, at least 60%, at least 65%, at least 70%, at least 75%, at least80%, at least 85%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, or at least 99% identical to SEQ ID NO: 14 or SEQ ID NO: 27. Insome embodiments that may be combined with any of the precedingembodiments, the second amino acid sequence includes an amino acidsequence that is 100% identical to SEQ ID NO: 14 or SEQ ID NO: 27. Insome embodiments that may be combined with any of the precedingembodiments, the recombinant polypeptide interacts with an RNApolymerase. In some embodiments, the RNA polymerase is RNA polymerase V.In some embodiments that may be combined with any of the precedingembodiments, the recombinant polypeptide induces RNA-directed DNAmethylation. In some embodiments that may be combined with any of thepreceding embodiments, the one or more target nucleic acids areendogenous nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, expression of the one or moretarget nucleic acids is silenced. In some embodiments that may becombined with any of the preceding embodiments, the method includesproviding a plant that further includes an additional recombinantnucleic acid, where the additional recombinant nucleic acid encodes arecombinant polypeptide including a first amino acid sequence includinga DNA-binding domain and a second amino acid sequence including an SHH1polypeptide or a fragment thereof; and growing the plant underconditions where the additional recombinant polypeptide encoded by theadditional recombinant nucleic acid is expressed and binds to the one ormore target nucleic acids, thereby reducing expression of the one ormore target nucleic acids.

The present disclosure further relates to a recombinant nucleic acidencoding a SUVH2-like protein or a SUVH9-like protein including a firstamino acid sequence including a DNA-binding domain and a second aminoacid sequence including a SUVH2 polypeptide or a fragment thereof, or aSUVH9 polypeptide or a fragment thereof. In some embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 14 or SEQ IDNO: 27. In some embodiments, the second amino acid sequence includes anamino acid sequence that is 100% identical to SEQ ID NO: 14 or SEQ IDNO: 27. In some embodiments that may be combined with any of thepreceding embodiments, the DNA-binding domain includes a zinc fingerdomain. In some embodiments, the zinc finger domain includes two, three,four, five, six, seven, eight, or nine zinc fingers. In someembodiments, the zinc finger domain is a zinc finger array. In someembodiments, the zinc finger domain is selected from a C2H2 zinc fingerdomain, a CCCH zinc finger domain, a multi-cysteine zinc finger domain,and a zinc binuclear cluster domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainis selected from a TAL effector targeting domain, a helix-turn-helixfamily DNA-binding domain, a basic domain, a ribbon-helix-helix domain,a TBP domain, a barrel dimer domain, a real homology domain, a BAHdomain, a SANT domain, a Chromodomain, a Tudor domain, a Bromodomain, aPHD domain, a WD40 domain, and a MBD domain. In some embodiments thatmay be combined with any of the preceding embodiments, the DNA-bindingdomain includes a TAL effector targeting domain. In some embodimentsthat may be combined with any of the preceding embodiments, theDNA-binding domain binds one or more target nucleic acids. In someembodiments that may be combined with any of the preceding embodiments,the DNA-binding domain binds one or more target nucleic acids. In someembodiments, the one or more target nucleic acids arepolypeptide-encoding nucleic acids. In some embodiments, the one or moretarget nucleic acids are endogenous plant nucleic acids. In someembodiments, the one or more target nucleic acids are heterologousnucleic acids. In some embodiments that may be combined with any of thepreceding embodiments, the SUVH2-like protein and/or the SUVH9-likeprotein reduces expression of the one or more target nucleic acids. Insome embodiments that may be combined with any of the precedingembodiments, the SUVH2-like protein and/or the SUVH9-like proteinsilences expression of the one or more target nucleic acids.

Other aspects of the present disclosure relate to a vector containingthe recombinant nucleic acid encoding the SUVH2-like protein and/or theSUVH9-like protein of any of the preceding embodiments, where therecombinant nucleic acid is operably linked to a regulatory sequence.Other aspects of the present disclosure relate to a host cell containingthe expression vector of the preceding embodiment. In certainembodiments, the host cell is a plant cell. Other aspects of the presentdisclosure relate to a recombinant plant containing the recombinantnucleic acid of any of the preceding embodiments.

The present disclosure is further related to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant including a first recombinant nucleic acid encoding afirst recombinant polypeptide including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding an SHH1 polypeptide or a fragment thereof, and a secondrecombinant nucleic acid encoding a second recombinant polypeptideincluding a first amino acid sequence including a DNA-binding domain anda second amino acid sequence including a SUVH2 polypeptide or a fragmentthereof, or a SUVH9 polypeptide or a fragment thereof; and b) growingthe plant under conditions where the first recombinant polypeptideencoded by the first recombinant nucleic acid and the second recombinantpolypeptide encoded by the second recombinant nucleic acid are expressedand bind to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain of at least one of the recombinant polypeptidesincludes a zinc finger domain. In some embodiments, the zinc fingerdomain includes two, three, four, five, six, seven, eight, or nine zincfingers. In some embodiments, the zinc finger domain is a zinc fingerarray. In some embodiments, the zinc finger domain is selected from aCys2His2 (C2H2) zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain from at least one of the recombinantpolypeptides is selected from a TAL effector targeting domain, ahelix-turn-helix family DNA-binding domain, a basic domain, aribbon-helix-helix domain, a TBP domain, a barrel dimer domain, a realhomology domain, a BAH domain, a SANT domain, a Chromodomain, a Tudordomain, a Bromodomain, a PHD domain, a WD40 domain, and a MBD domain. Insome embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain of at least one of the recombinantpolypeptides includes a TAL effector targeting domain. In someembodiments that may be combined with any of the preceding embodiments,the DNA-binding domain of at least one of the recombinant polypeptidesincludes three C2H2 zinc finger domains. In some embodiments that may becombined with any of the preceding embodiments, the second amino acidsequence of the first recombinant polypeptide includes at least one of ahomeodomain or a SAWADEE domain. In some embodiments that may becombined with any of the preceding embodiments, the second amino acidsequence of the first recombinant polypeptide includes an amino acidsequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 1. In some embodiments that may be combined with any of thepreceding embodiments, the second amino acid sequence of the firstrecombinant polypeptide includes an amino acid sequence that is 100%identical to SEQ ID NO: 1. In some embodiments that may be combined withany of the preceding embodiments, at least one of the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments, theRNA polymerase is RNA polymerase IV. In some embodiments that may becombined with any of the preceding embodiments, the first recombinantpolypeptide interacts with methylated H3K9. In some embodiments that maybe combined with any of the preceding embodiments, the first recombinantpolypeptide interacts with H3K9me1, H3K9me2, and/or H3K9me3. In someembodiments that may be combined with any of the preceding embodiments,the first recombinant polypeptide induces RNA-directed DNA methylation.In some embodiments that may be combined with any of the precedingembodiments, the second amino acid sequence of the second recombinantpolypeptide includes a domain selected from a two-helix bundle domain, aSRA domain, a pre-SET domain, or a SET domain. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence from the second recombinant polypeptide includes an aminoacid sequence that is at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, or at least 99% identicalto SEQ ID NO: 14 or SEQ ID NO: 27. In some embodiments that may becombined with any of the preceding embodiments, the second amino acidsequence of the second recombinant polypeptide includes an amino acidsequence that is 100% identical to SEQ ID NO: 14 or SEQ ID NO: 27. Insome embodiments that may be combined with any of the precedingembodiments, the second recombinant polypeptide interacts with an RNApolymerase. In some embodiments, the RNA polymerase is RNA polymerase V.In some embodiments that may be combined with any of the precedingembodiments, the second recombinant polypeptide induces RNA-directed DNAmethylation. In some embodiments that may be combined with any of thepreceding embodiments, at least one of the recombinant polypeptidesinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, the one ormore target nucleic acids is silenced.

Other aspects of the present disclosure relate to a vector containingthe recombinant nucleic acid encoding the SHH1-like protein, theSUVH2-like protein and/or the SUVH9-like protein of any of the precedingembodiments, where the recombinant nucleic acid is operably linked to aregulatory sequence. Other aspects of the present disclosure relate to ahost cell containing the expression vectors of the preceding embodiment.In certain embodiments, the host cell is a plant cell. Other aspects ofthe present disclosure relate to a recombinant plant containing therecombinant nucleic acids of any of the preceding embodiments.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including a DMS3 polypeptide or a fragment thereof;and b) growing the plant under conditions where the recombinantpolypeptide encoded by the recombinant nucleic acid is expressed andbinds to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a Cys2His2 (C2H2) zinc finger domain, aCCCH zinc finger domain, a multi-cysteine zinc finger domain, and a zincbinuclear cluster domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain is selectedfrom a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainincludes a TAL effector targeting domain. In some embodiments that maybe combined with any of the preceding embodiments, the DNA-bindingdomain includes three C2H2 zinc finger domains. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence includes a domain selected from a two-helix bundle domain,a SRA domain, a pre-SET domain, or a SET domain. In some embodimentsthat may be combined with any of the preceding embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 41. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that is100% identical to SEQ ID NO: 41. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments thatmay be combined with any of the preceding embodiments, the RNApolymerase is RNA polymerase V. In some embodiments that may be combinedwith any of the preceding embodiments, the recombinant polypeptideinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, expressionof the one or more target nucleic acids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding a DMS3-like protein including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding a DMS3 polypeptide or a fragment thereof. In some embodiments,the second amino acid sequence includes an amino acid sequence that isat least 50%, at least 55%, at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identical to SEQ ID NO: 41. Insome embodiments, the second amino acid sequence includes an amino acidsequence that is 100% identical to SEQ ID NO: 41. In some embodimentsthat may be combined with any of the preceding embodiments, theDNA-binding domain includes a zinc finger domain. In some embodiments,the zinc finger domain includes two, three, four, five, six, seven,eight, or nine zinc fingers. In some embodiments, the zinc finger domainis a zinc finger array. In some embodiments, the zinc finger domain isselected from a C2H2 zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain is selected from a TAL effectortargeting domain, a helix-turn-helix family DNA-binding domain, a basicdomain, a ribbon-helix-helix domain, a TBP domain, a barrel dimerdomain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the DMS3-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, theDMS3-like protein silences expression of the one or more target nucleicacids.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including a MORC6 polypeptide or a fragment thereof;and b) growing the plant under conditions where the recombinantpolypeptide encoded by the recombinant nucleic acid is expressed andbinds to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a Cys2His2 (C2H2) zinc finger domain, aCCCH zinc finger domain, a multi-cysteine zinc finger domain, and a zincbinuclear cluster domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain is selectedfrom a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainincludes a TAL effector targeting domain. In some embodiments that maybe combined with any of the preceding embodiments, the DNA-bindingdomain includes three C2H2 zinc finger domains. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence includes a domain selected from a two-helix bundle domain,a SRA domain, a pre-SET domain, or a SET domain. In some embodimentsthat may be combined with any of the preceding embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 53. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that is100% identical to SEQ ID NO: 53. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments thatmay be combined with any of the preceding embodiments, the RNApolymerase is RNA polymerase V. In some embodiments that may be combinedwith any of the preceding embodiments, the recombinant polypeptideinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, expressionof the one or more target nucleic acids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding a MORC6-like protein including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding a MORC6 polypeptide or a fragment thereof. In someembodiments, the second amino acid sequence includes an amino acidsequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 53. In some embodiments, the second amino acid sequence includesan amino acid sequence that is 100% identical to SEQ ID NO: 53. In someembodiments that may be combined with any of the preceding embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a C2H2 zinc finger domain, a CCCH zincfinger domain, a multi-cysteine zinc finger domain, and a zinc binuclearcluster domain. In some embodiments that may be combined with any of thepreceding embodiments, the DNA-binding domain is selected from a TALeffector targeting domain, a helix-turn-helix family DNA-binding domain,a basic domain, a ribbon-helix-helix domain, a TBP domain, a barreldimer domain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the MORC6-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, theMORC6-like protein silences expression of the one or more target nucleicacids.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including a SUVR2 polypeptide or a fragment thereof;and b) growing the plant under conditions where the recombinantpolypeptide encoded by the recombinant nucleic acid is expressed andbinds to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a Cys2His2 (C2H2) zinc finger domain, aCCCH zinc finger domain, a multi-cysteine zinc finger domain, and a zincbinuclear cluster domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain is selectedfrom a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainincludes a TAL effector targeting domain. In some embodiments that maybe combined with any of the preceding embodiments, the DNA-bindingdomain includes three C2H2 zinc finger domains. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence includes a domain selected from a two-helix bundle domain,a SRA domain, a pre-SET domain, or a SET domain. In some embodimentsthat may be combined with any of the preceding embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 66. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that is100% identical to SEQ ID NO: 66. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments thatmay be combined with any of the preceding embodiments, the RNApolymerase is RNA polymerase V. In some embodiments that may be combinedwith any of the preceding embodiments, the recombinant polypeptideinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, expressionof the one or more target nucleic acids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding a SUVR2-like protein including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding a SUVR2 polypeptide or a fragment thereof. In someembodiments, the second amino acid sequence includes an amino acidsequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 66. In some embodiments, the second amino acid sequence includesan amino acid sequence that is 100% identical to SEQ ID NO: 66. In someembodiments that may be combined with any of the preceding embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a C2H2 zinc finger domain, a CCCH zincfinger domain, a multi-cysteine zinc finger domain, and a zinc binuclearcluster domain. In some embodiments that may be combined with any of thepreceding embodiments, the DNA-binding domain is selected from a TALeffector targeting domain, a helix-turn-helix family DNA-binding domain,a basic domain, a ribbon-helix-helix domain, a TBP domain, a barreldimer domain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the SUVR2-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, theSUVR2-like protein silences expression of the one or more target nucleicacids.

Other aspects of the present disclosure relate to a vector containingthe recombinant nucleic acid encoding a DMS3-like, MORC6-like, and/orSUVR2-like protein of any of the preceding embodiments, where therecombinant nucleic acid is operably linked to a regulatory sequence.Other aspects of the present disclosure relate to a host cell containingthe expression vector of the preceding embodiment. In certainembodiments, the host cell is a plant cell. Other aspects of the presentdisclosure relate to a recombinant plant containing the recombinantnucleic acid of any of the preceding embodiments.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including:(a) providing a plant including a first recombinant nucleic acidencoding a first recombinant polypeptide including a first amino acidsequence including a DNA-binding domain and a second amino acid sequenceincluding an SHH1 polypeptide or a fragment thereof, and one or moreadditional recombinant nucleic acids encoding one or more additionalpolypeptides, each of the one or more additional polypeptides includinga first amino acid sequence including a DNA-binding domain and a secondamino acid sequence including a polypeptide selected from the groupconsisting of a SUVH2 polypeptide or a fragment thereof, a SUVH9polypeptide or a fragment thereof, a DMS3 polypeptide or a fragmentthereof, a MORC6 polypeptide or a fragment thereof, a SUVR2 polypeptideor a fragment thereof, a DRD1 polypeptide or a fragment thereof, an RDM1polypeptide or a fragment thereof, a DRM3 polypeptide or a fragmentthereof, a DRM2 polypeptide or a fragment thereof, and an FRGpolypeptide or a fragment thereof and; and (b) growing the plant underconditions where the first recombinant polypeptide encoded by the firstrecombinant nucleic acid and the one or more additional polypeptidesencoded by the one or more additional recombinant nucleic acids areexpressed and bind to the one or more target nucleic acids, therebyreducing expression of the one or more target nucleic acids. In someembodiments, at least one of the recombinant polypeptides inducesRNA-directed DNA methylation. In some embodiments, the one or moretarget nucleic acids are endogenous nucleic acids. In some embodiments,the one or more target nucleic acids are heterologous nucleic acids. Insome embodiments, expression of the one or more target nucleic acids issilenced.

Other aspects of the disclosure relate to a host cell includingexpression vectors including the recombinant nucleic acids encoding therecombinant polypeptides of any one of the preceding embodiments. Insome embodiments, the host cell is a plant cell. Other aspects of thedisclosure relate to a recombinant plant including the recombinantnucleic acids of any one of the preceding embodiments.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, includingproviding a plant including: (a) a small interfering RNA (siRNA) whichtargets one or more target nucleic acids, and one or more recombinantnucleic acids encoding one or more polypeptides, each of the one or morepolypeptides including a first amino acid sequence including aDNA-binding domain and a second amino acid sequence including apolypeptide selected from the group consisting of a SUVH2 polypeptide ora fragment thereof, a SUVH9 polypeptide or a fragment thereof, a DMS3polypeptide or a fragment thereof, a MORC6 polypeptide or a fragmentthereof, a SUVR2 polypeptide or a fragment thereof, a DRD1 polypeptideor a fragment thereof, an RDM1 polypeptide or a fragment thereof, a DRM3polypeptide or a fragment thereof, a DRM2 polypeptide or a fragmentthereof, and an FRG polypeptide or a fragment thereof and (b) growingthe plant under conditions whereby the siRNA interacts with the one ormore target nucleic acids and the one or more polypeptides encoded bythe one or more recombinant nucleic acids are expressed and bind to theone or more target nucleic acids, thereby reducing expression of the oneor more target nucleic acids.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including a DRD1 polypeptide or a fragment thereof;and b) growing the plant under conditions where the recombinantpolypeptide encoded by the recombinant nucleic acid is expressed andbinds to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a Cys2His2 (C2H2) zinc finger domain, aCCCH zinc finger domain, a multi-cysteine zinc finger domain, and a zincbinuclear cluster domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain is selectedfrom a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainincludes a TAL effector targeting domain. In some embodiments that maybe combined with any of the preceding embodiments, the DNA-bindingdomain includes three C2H2 zinc finger domains. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence includes a domain selected from a two-helix bundle domain,a SRA domain, a pre-SET domain, or a SET domain. In some embodimentsthat may be combined with any of the preceding embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 79. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that is100% identical to SEQ ID NO: 79. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments thatmay be combined with any of the preceding embodiments, the RNApolymerase is RNA polymerase V. In some embodiments that may be combinedwith any of the preceding embodiments, the recombinant polypeptideinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, expressionof the one or more target nucleic acids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding a DRD1-like protein including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding a DRD1 polypeptide or a fragment thereof. In some embodiments,the second amino acid sequence includes an amino acid sequence that isat least 50%, at least 55%, at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identical to SEQ ID NO: 79. Insome embodiments, the second amino acid sequence includes an amino acidsequence that is 100% identical to SEQ ID NO: 79. In some embodimentsthat may be combined with any of the preceding embodiments, theDNA-binding domain includes a zinc finger domain. In some embodiments,the zinc finger domain includes two, three, four, five, six, seven,eight, or nine zinc fingers. In some embodiments, the zinc finger domainis a zinc finger array. In some embodiments, the zinc finger domain isselected from a C2H2 zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain is selected from a TAL effectortargeting domain, a helix-turn-helix family DNA-binding domain, a basicdomain, a ribbon-helix-helix domain, a TBP domain, a barrel dimerdomain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the DRD1-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, theDRD1-like protein silences expression of the one or more target nucleicacids.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including an RDM1 polypeptide or a fragment thereof;and b) growing the plant under conditions where the recombinantpolypeptide encoded by the recombinant nucleic acid is expressed andbinds to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a Cys2His2 (C2H2) zinc finger domain, aCCCH zinc finger domain, a multi-cysteine zinc finger domain, and a zincbinuclear cluster domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain is selectedfrom a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainincludes a TAL effector targeting domain. In some embodiments that maybe combined with any of the preceding embodiments, the DNA-bindingdomain includes three C2H2 zinc finger domains. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence includes a domain selected from a two-helix bundle domain,a SRA domain, a pre-SET domain, or a SET domain. In some embodimentsthat may be combined with any of the preceding embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 91. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that is100% identical to SEQ ID NO: 91. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments thatmay be combined with any of the preceding embodiments, the RNApolymerase is RNA polymerase V. In some embodiments that may be combinedwith any of the preceding embodiments, the recombinant polypeptideinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, expressionof the one or more target nucleic acids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding an RDM1-like protein including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding an RDM1 polypeptide or a fragment thereof. In someembodiments, the second amino acid sequence includes an amino acidsequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or at least 99% identical to SEQID NO: 91. In some embodiments, the second amino acid sequence includesan amino acid sequence that is 100% identical to SEQ ID NO: 91. In someembodiments that may be combined with any of the preceding embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a C2H2 zinc finger domain, a CCCH zincfinger domain, a multi-cysteine zinc finger domain, and a zinc binuclearcluster domain. In some embodiments that may be combined with any of thepreceding embodiments, the DNA-binding domain is selected from a TALeffector targeting domain, a helix-turn-helix family DNA-binding domain,a basic domain, a ribbon-helix-helix domain, a TBP domain, a barreldimer domain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the RDM1-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, theRDM1-like protein silences expression of the one or more target nucleicacids.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including a DRM3 polypeptide or a fragment thereof;and b) growing the plant under conditions where the recombinantpolypeptide encoded by the recombinant nucleic acid is expressed andbinds to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a Cys2His2 (C2H2) zinc finger domain, aCCCH zinc finger domain, a multi-cysteine zinc finger domain, and a zincbinuclear cluster domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain is selectedfrom a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainincludes a TAL effector targeting domain. In some embodiments that maybe combined with any of the preceding embodiments, the DNA-bindingdomain includes three C2H2 zinc finger domains. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence includes a domain selected from a two-helix bundle domain,a SRA domain, a pre-SET domain, or a SET domain. In some embodimentsthat may be combined with any of the preceding embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75% at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 101. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that is100% identical to SEQ ID NO: 101. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments thatmay be combined with any of the preceding embodiments, the RNApolymerase is RNA polymerase V. In some embodiments that may be combinedwith any of the preceding embodiments, the recombinant polypeptideinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, expressionof the one or more target nucleic acids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding a DRM3-like protein including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding a DRM3 polypeptide or a fragment thereof. In some embodiments,the second amino acid sequence includes an amino acid sequence that isat least 50%, at least 55%, at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identical to SEQ ID NO: 101. Insome embodiments, the second amino acid sequence includes an amino acidsequence that is 100% identical to SEQ ID NO: 101. In some embodimentsthat may be combined with any of the preceding embodiments, theDNA-binding domain includes a zinc finger domain. In some embodiments,the zinc finger domain includes two, three, four, five, six, seven,eight, or nine zinc fingers. In some embodiments, the zinc finger domainis a zinc finger array. In some embodiments, the zinc finger domain isselected from a C2H2 zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain is selected from a TAL effectortargeting domain, a helix-turn-helix family DNA-binding domain, a basicdomain, a ribbon-helix-helix domain, a TBP domain, a barrel dimerdomain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the DRM3-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, theDRM3-like protein silences expression of the one or more target nucleicacids.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including a DRM2 polypeptide or a fragment thereof;and b) growing the plant under conditions where the recombinantpolypeptide encoded by the recombinant nucleic acid is expressed andbinds to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a Cys2His2 (C2H2) zinc finger domain, aCCCH zinc finger domain, a multi-cysteine zinc finger domain, and a zincbinuclear cluster domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain is selectedfrom a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainincludes a TAL effector targeting domain. In some embodiments that maybe combined with any of the preceding embodiments, the DNA-bindingdomain includes three C2H2 zinc finger domains. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence includes a domain selected from a two-helix bundle domain,a SRA domain, a pre-SET domain, or a SET domain. In some embodimentsthat may be combined with any of the preceding embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 113. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that is100% identical to SEQ ID NO: 113. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments thatmay be combined with any of the preceding embodiments, the RNApolymerase is RNA polymerase V. In some embodiments that may be combinedwith any of the preceding embodiments, the recombinant polypeptideinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, expressionof the one or more target nucleic acids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding a DRM2-like protein including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding a DRM2 polypeptide or a fragment thereof. In some embodiments,the second amino acid sequence includes an amino acid sequence that isat least 50%, at least 55%, at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identical to SEQ ID NO: 113. Insome embodiments, the second amino acid sequence includes an amino acidsequence that is 100% identical to SEQ ID NO: 113. In some embodimentsthat may be combined with any of the preceding embodiments, theDNA-binding domain includes a zinc finger domain. In some embodiments,the zinc finger domain includes two, three, four, five, six, seven,eight, or nine zinc fingers. In some embodiments, the zinc finger domainis a zinc finger array. In some embodiments, the zinc finger domain isselected from a C2H2 zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain is selected from a TAL effectortargeting domain, a helix-turn-helix family DNA-binding domain, a basicdomain, a ribbon-helix-helix domain, a TBP domain, a barrel dimerdomain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the DRM2-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, theDRM2-like protein silences expression of the one or more target nucleicacids.

The present disclosure further relates to a method for reducingexpression of one or more target nucleic acids in a plant, including: a)providing a plant containing a recombinant nucleic acid, wherein therecombinant nucleic acid encodes a recombinant polypeptide including afirst amino acid sequence including a DNA-binding domain and a secondamino acid sequence including an FRG polypeptide or a fragment thereof;and b) growing the plant under conditions where the recombinantpolypeptide encoded by the recombinant nucleic acid is expressed andbinds to the one or more target nucleic acids, thereby reducingexpression of the one or more target nucleic acids. In some embodiments,the DNA-binding domain includes a zinc finger domain. In someembodiments, the zinc finger domain includes two, three, four, five,six, seven, eight, or nine zinc fingers. In some embodiments, the zincfinger domain is a zinc finger array. In some embodiments, the zincfinger domain is selected from a Cys2His2 (C2H2) zinc finger domain, aCCCH zinc finger domain, a multi-cysteine zinc finger domain, and a zincbinuclear cluster domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain is selectedfrom a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain. In some embodiments that may becombined with any of the preceding embodiments, the DNA-binding domainincludes a TAL effector targeting domain. In some embodiments that maybe combined with any of the preceding embodiments, the DNA-bindingdomain includes three C2H2 zinc finger domains. In some embodiments thatmay be combined with any of the preceding embodiments, the second aminoacid sequence includes a domain selected from a two-helix bundle domain,a SRA domain, a pre-SET domain, or a SET domain. In some embodimentsthat may be combined with any of the preceding embodiments, the secondamino acid sequence includes an amino acid sequence that is at least50%, at least 55%, at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 85%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, or at least 99% identical to SEQ ID NO: 125. In someembodiments that may be combined with any of the preceding embodiments,the second amino acid sequence includes an amino acid sequence that is100% identical to SEQ ID NO: 125. In some embodiments that may becombined with any of the preceding embodiments, the recombinantpolypeptide interacts with an RNA polymerase. In some embodiments thatmay be combined with any of the preceding embodiments, the RNApolymerase is RNA polymerase V. In some embodiments that may be combinedwith any of the preceding embodiments, the recombinant polypeptideinduces RNA-directed DNA methylation. In some embodiments that may becombined with any of the preceding embodiments, the one or more targetnucleic acids are endogenous nucleic acids. In some embodiments that maybe combined with any of the preceding embodiments, the one or moretarget nucleic acids are heterologous nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, expressionof the one or more target nucleic acids is silenced.

The present disclosure further relates to a recombinant nucleic acidencoding an FRG-like protein including a first amino acid sequenceincluding a DNA-binding domain and a second amino acid sequenceincluding a FRG polypeptide or a fragment thereof. In some embodiments,the second amino acid sequence includes an amino acid sequence that isat least 50%, at least 55%, at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or at least 99% identical to SEQ ID NO: 125. Insome embodiments, the second amino acid sequence includes an amino acidsequence that is 100% identical to SEQ ID NO: 125. In some embodimentsthat may be combined with any of the preceding embodiments, theDNA-binding domain includes a zinc finger domain. In some embodiments,the zinc finger domain includes two, three, four, five, six, seven,eight, or nine zinc fingers. In some embodiments, the zinc finger domainis a zinc finger array. In some embodiments, the zinc finger domain isselected from a C2H2 zinc finger domain, a CCCH zinc finger domain, amulti-cysteine zinc finger domain, and a zinc binuclear cluster domain.In some embodiments that may be combined with any of the precedingembodiments, the DNA-binding domain is selected from a TAL effectortargeting domain, a helix-turn-helix family DNA-binding domain, a basicdomain, a ribbon-helix-helix domain, a TBP domain, a barrel dimerdomain, a real homology domain, a BAH domain, a SANT domain, aChromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40domain, and a MBD domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain includes a TALeffector targeting domain. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments that may be combined withany of the preceding embodiments, the DNA-binding domain binds one ormore target nucleic acids. In some embodiments, the one or more targetnucleic acids are polypeptide-encoding nucleic acids. In someembodiments, the one or more target nucleic acids are endogenous plantnucleic acids. In some embodiments, the one or more target nucleic acidsare heterologous nucleic acids. In some embodiments that may be combinedwith any of the preceding embodiments, the FRG-like protein reducesexpression of the one or more target nucleic acids. In some embodimentsthat may be combined with any of the preceding embodiments, the FRG-likeprotein silences expression of the one or more target nucleic acids.

Other aspects of the present disclosure relate to a plant having reducedexpression of one or more target nucleic acids according to the methodof any one of the preceding embodiments, as well as a progeny plant ofthe plant of the preceding embodiment. In some embodiments, the progenyplant has reduced expression of the one or more target nucleic acids anddoes not include the recombinant nucleic acids of the presentdisclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawings will be provided by the office upon request and paymentof the necessary fee.

FIG. 1A-FIG. 1G illustrate an epigenetic profile of sRNA clustersaffected in RdDM mutants. FIG. 1A illustrates a pie chart showing theabundance of 24 nt siRNA reads (U.S. Pat. No. 5,967,213 uniquely mappingreads total) within the indicated categories. FIG. 1B illustrates a Venndiagram showing the approximate relationships of 24 nt siRNA clustersreduced in each genotype and the subclasses used for downstreamanalysis. FIG. 1C illustrates pie charts showing the chromosomaldistribution (based on the previously described definitions ofpericentromeric heterochromatin and euchromatin) of affected siRNAclusters in the indicated subclasses. FIG. 1D and FIG. 1E illustrateboxplots of siRNA and CHH methylation patterns at the subclasses shownin FIG. 1B for the different RdDM mutants (* indicates significantreduction; P<1e-10 Mann-Whitney U test). FIG. 1F illustrates metaplotsshowing the enrichment of CMT3, and Pol-V at affected siRNA clusters(+/−5000 bp from the midpoint of the sRNA cluster). FIG. 1G illustratesheatmaps of Pol-V enrichment over affected siRNA clusters.

FIG. 2A-FIG. 2B illustrate Polymerase IV levels at defined siRNAclusters. FIG. 2A illustrates metaplots and FIG. 2B illustrates heatmapsof Pol-IV enrichment over the defined siRNA clusters in the indicatedgenetic backgrounds. Metaplots and heatmaps extend+/−5000 bp from themidpoint of the siRNA cluster.

FIG. 3A-FIG. 3D illustrate that the SHH1 SAWADEE domain recognizes H3K9methylation and adopts a unique tandem Tudor domain-like fold. FIG. 3Aand FIG. 3B illustrates ITC-based measurements of the SAWADEE domainbinding to the modified or unmodified histone peptides as indicated.K_(d) values are listed. FIG. 3C illustrates metaplot analyses showingthe enrichment of H3K9me2 over the indicated Pol-IV ChIP-seq peakclasses. FIG. 3D illustrates the overall structure of SHH1 SAWADEEdomain in the free form. The two tandem Tudor domains are shown inmagenta (Tudor 1) and green (Tudor 2). The unique zinc-binding motif ofthe SAWADEE domain is shown as an enlarged ball-and-stick model,highlighting the details of the metal coordination. A bound detergentmolecule 4-Cyclohexyl-1-Butyl-β-D-Maltoside (CYMAL®-4, Hampton Research)moiety from the crystallization condition is shown in yellow in a stickrepresentation.

FIG. 4A-FIG. 4J illustrate the structural basis for recognition ofH3(1-15)K9me2 peptide by the SHH1 SAWADEE domain and in vivo functionanalyses. FIG. 4A illustrates the overall structure of theH3(1-15)K9me2-SAWADEE complex. The SAWADEE domain is shown as a ribbondiagram and the peptide in a stick representation. The simulatedannealing composite omit electron density map at 1σ level of the boundpeptide is also shown. Tudor domains 1 and 2 are shown in magenta andgreen, respectively. FIG. 4B illustrates a stereo view highlighting thedetails of the intermolecular interactions between the SAWADEE domainand the bound H3(1-15)K9me2 peptide. Intermolecular hydrogen-bondinginteractions are designated by dashed red lines. The aromatic cage,which recognizes the dimethylated K9, is also shown. FIG. 4C illustratesa representation of the intermolecular interactions between the SAWADEEdomain and the bound H3(1-15)K9me2 peptide. FIG. 4D illustrates asuperposition of the H3K9me2 peptide bound SAWADEE domain (with Tudorlin magenta and Tudor 2 in green) and the free form of the SAWADEE domain(in silver) reveals no significant overall conformational change uponpeptide binding. FIG. 4E illustrates that the unmethylated K4 insertsinto a narrow pocket formed by Glu130 and Asp141 from Tudor 1, andLeu201 and Tyr212 from Tudor 2, and forms two hydrogen bonds with Glu130and Asp141, as well as electrostatics interactions. FIG. 4F illustratesa detailed view of the recognition of the dimethylated K9 by an aromaticcage formed by three aromatic residues. FIG. 4G illustrates that themonomethylated K4 is tolerated by the K4 binding pocket of SAWADEEdomain as revealed by the crystal structure of theH3(1-15)K4me1K9me1-SAWADEE complex. The additional methyl group disruptsone hydrogen bond with Glu130 and introduces more van der Waals contactswith other residues. FIG. 4H and FIG. 4I illustrate boxplots showing the% CHH methylation and siRNA levels respectively, in wild-type andshh/mutants as well as shh/mutants transformed with SHH1 constructs witheither the wild-type SHH1 sequence or point mutations in the K9(F162AF165A and Y140A) or K4 (D141A and Y212A) binding pockets. (*indicates significant reduction; P<1e-10 Mann-Whitney U test). FIG. 4Jillustrates quantitative PCR results showing enrichment of Pol-IV inwild-type and SHH1 mutant backgrounds. Blue bars indicate the average oftwo biological replicates after normalization to input and the level ofactin. Black bars indicate the Standard error.

FIG. 5A-FIG. 5F illustrate that SUVH2 and SUVH9 are required for Pol Vchromatin binding, transcription, and resulting DNA methylation. FIG. 5Aillustrates quantitative PCR (qPCR) of IGN22 and P6 relative to ACTIN7and normalized to Columbia (WT). Mean+/−standard deviation (SD) of twobiological replicas. FIG. 5B illustrates qPCR of IGN22 and IGN5 fromFlag ChIP shown as enrichment of IP/input relative to ACTIN7 inNRPE1-Flag/WT and NRPE1-Flag/suvh2suvh9 lines. Mean+/−SD of twobiological replicas. FIG. 5C illustrates a heat map of NRPE1 enrichmentat defined NRPE1 sites determined by Flag ChIP-seq in eitherNRPE1-Flag/WT or NRPE1-Flag/suvh2suvh9, with Flag ChIP in Columbia asnegative control. FIG. 5D illustrates box plot (whiskers extend to ±1.5interquartile range (IQR)) of NRPE1 enrichment at sites shown in C forNRPE1-Flag/WT and NRPE1-Flag/suvh2suvh9. FIG. 5E illustrates the percentmethylation at all defined NRPE1 binding sites (mean+/−SD) as determinedby whole-genome bisulfite sequencing. FIG. 5F illustrates the density ofH3K9me1 ChIP-seq reads in WT, suvh2suvh9, and suvh4suvh5suvh6,normalized by the mean histone methylation level at 80 selectedeuchromatic sites.

FIG. 6A-FIG. 6E illustrate that tethered SUVH2 attracts DNA methylationand causes late-flowering phenotype. FIG. 6A, top illustrates a diagramof SUVH2 with Zn Finger inserted immediately before the HA tag at theN-terminus. FIG. 6A, bottom illustrates a schematic of FWA gene showingthe two small and two large repeats (blue arrows), the regions amplifiedby PCR (promoter and transcript), the start of transcription (red arrow)and the sites bound by the Zn finger (indicated by two orange arrows).FIG. 6B illustrates plants grown side-by-side to illustrate earlyflowering of ZF-SUVH2 in fwa-4 (T2 plants) compared to fwa-4. FIG. 6Cillustrates flowering time of Columbia (WT), ZF-SUVH2 in fwa-4, HA-SUVH2in fwa-4 and fwa-4. Mean+/−SD. FIG. 6D illustrates percent methylationat each C in the FWA repeat region. Numbers indicate individual Cresidues, two black lines show location of ZF binding sites, red arrowshows the location of transcript. Percent methylation was determinedfrom 20-25 clones of bisulfite-treated DNA. FIG. 6E illustrates percentmethylation at each C in the FWA repeat region from three individual T1plants.

FIG. 7A-FIG. 7C illustrate that ZF-SUVH2 recruits Pol V, but not histonemethylation, to FWA. FIG. 7A illustrates NRPE1 ChIP in WT (positivecontrol), carpel mutant (negative control), fwa-4 epiallele, andZF-SUVH2/fwa-4. qPCR of two characterized NRPE sites (IGN5 and IGN22)and two regions in FWA (FWAp-promoter and FWAt-transcript) shown asenrichment of IP/input relative to negative control. Mean+/−SD of twobiological replicas. FIG. 7B illustrates H3K9me1 ChIP in WT, fwa-4 andZF-SUVH2/fwa-4 T1 flowers. Negative control is a region in euchromatindevoid of DNA methylation. Enrichment is relative to the heterochromaticretrotransposon Ta3. Mean+/−SD of two biological replicas. FIG. 7Cillustrates the same as FIG. 7B, but ZF-SUVH2/fwa-4 was from T2 flowers.

FIG. 8A-FIG. 8H illustrate the crystal structure of SUVH9 in the freestate and interactions between domains. FIG. 8A illustrates acolor-coded schematic representation of full length SUVH9 and theN-terminally truncated construct used for crystallization. FIG. 8Billustrates a ribbon diagram of the crystal structure of SUVH9containing a two-helix bundle towards the N-terminus, the SRA domain,the pre-SET domain, and the SET domain colored in pink, green, orange,and blue, respectively. The disordered regions are shown with dashedlines. The Zn₃Cys₉ cluster (bottom right of panel) is highlighted withball-and-stick model. FIG. 8C illustrates the hydrophobic interactionsand charged interactions within the two-helix bundle shown in twoalternate views rotated by 180°. Residues involved in inter-helixhydrophobic interactions are highlighted in yellow. FIG. 8D illustratesthe N-terminal part of the first α-helix forms charged and hydrogenbonding interactions with the SRA domain and the SET domain. Theinteracting residues are shown in stick representation and thehydrogen-bonding interactions are shown with dashed red lines. FIG. 8Eillustrates the C-terminal part of the first α-helix exhibits extensivehydrophobic interactions with the SRA domain and the pre-SET/SETdomains. The tip of a long loop from the SET domain covers over thefirst α-helix and forms hydrophobic interactions with it. Theinteracting residues are shown in a stick representation. FIG. 8Fillustrates the second α-helix forms some interactions with the SRAdomain. The interacting residues are shown in stick representation andthe hydrogen bonding interactions are shown with red dashes. FIG. 8Gillustrates the SRA domain forms a hydrophobic core that interacts withthe pre-SET/SET domains and the two-helix bundle. The interactingresidues are shown in a stick representation. FIG. 8H illustrates a longinsertion loop of SUVH9 SET domain (highlighted in magenta) is enrichedwith hydrophobic residues and forms extensive hydrophobic interactionswith the two-helix bundle, the pre-SET and SET domains.

FIG. 9A-FIG. 9E illustrate the structural comparison of SAH- andpeptide-bound GLP and SUVH9 in the free state and structural basisunderlying lack of methyltransferase activity for SUVH9. FIG. 9Aillustrates the crystal structure of human GLP in complex with bound SAH(PDB code: 2IGQ) is shown in a silver ribbon representation in the toppanel, with an expanded view of its SAH binding site shown in anelectrostatic surface representation in the bottom panel. The cofactorSAH is shown in a space-filling representation in both panels. The SAHbinding pocket of GLP is relatively narrow and binds to SAH withstructural and shape complementarity. FIG. 9B illustrates the crystalstructure of SUVH9 in the free-state is shown in a color-coded ribbonrepresentation in the top panel, with an expanded view of the putativeSAH binding site shown in an electrostatic surface representation in thebottom panel. The putative SAH binding pocket of SUVH9 is relativelyopen and does not provide a good fit for the SAH molecule. FIG. 9Cillustrates the crystal structure of human GLP in complex with SAH andH3K9me2 peptide (PDB code: 2RFI) is shown in silver ribbonrepresentation in the top panel, with an expanded view of its peptidebinding site shown in an electrostatic surface representation in thebottom panel. The post-SET domain and the acidic loop of the SET domaininvolved in peptide substrate binding are highlighted in cyan and darkblue, respectively. The bound peptide is shown in a space-fillingrepresentation in both panels. The peptide is bound in a surface cleftbetween the post-SET and SET domains. FIG. 9D illustrates the crystalstructure of SUVH9 in the free state is shown in a color-coded ribbonrepresentation in the top panel, with an expanded view of the putativepeptide-binding site shown in an electrostatic surface representation inthe bottom panel. The long insertion loop of the SET domain ishighlighted in magenta. The putative peptide-binding site is partiallyblocked by the long insertion loop and the there is no significantpeptide-binding cleft on the protein surface. FIG. 9E illustrates amodel positioning the mCHH DNA to the active site of SUVH9 SRA domainfollowing superposition the structures of the SUVH5 SRA-mCHH complex[PDB code: 3Q0F) and SUVH9 in the free-state. The DNA fits well into theSRA domain without significant steric clashes. Some surrounding residueson the second α-helix the two-helix bundle, which can potentially beinvolved in the binding to the DNA, are highlighted in a stickrepresentation.

FIG. 10 illustrates structure based sequence alignment of Arabidopsisthaliana SHH1, SHH2, and the SAWADEE domains from SHHlorthologs in otherspecies, including Ricinus communis, Vitis vinifera, Picea sitchensis,and Zea mays. The tandem Tudor domain of human UHRF1 is also includedfor comparison. The secondary structure of the SHH1 SAWADEE domain andthe human UHRF1 tandem Tudor domain are presented on the top and bottomof the alignment, respectively. The partially conserved hydrophobicresidues of the SAWADEE domain involved in binding the nonpolar tail ofthe detergent are marked by green stars. The conserved aromatic residuesinvolved in recognition of methylated K9 are marked by purple hexagons.The conserved SAWADEE residues involved in coordinating the zinc ion aremarked by black circles.

FIG. 11 illustrates structure-based sequence alignment of SUVH familyproteins from Arabidopsis. The secondary structural elements of SUVH9are labeled on the top of the sequence alignment. The domain boundariesare marked on the top. Conserved residues involved in the interactionwith flipped 5mC base and the DNA backbone available from the publishedSUVH5-DNA complex structures are highlighted with cyan circles and bluehexagons, respectively. The insertions in the SET domains arehighlighted with a purple box. The zinc-coordinating Cys residues arehighlighted with black stars in the SET domain and grey stars in thepost-SET domain. Two-tyrosine residues that are conserved and normallyimportant for enzymatic activity are highlighted with red dots.

FIG. 12A-FIG. 12C illustrate that SUVH2 and SUVH9 act redundantlygenome-wide. FIG. 12A illustrates metaplots of CHH methylation over DMRsidentified in the various SUVH mutants. FIG. 12B illustrates metaplotsof CHH methylation over Pol V binding sites. FIG. 12C illustrates a Venndiagram detailing the overlaps between CHH hypo-methylated regions inSUVH mutants.

FIG. 13A-FIG. 13E illustrate that Pol V binding is dependent on DNAmethylation. FIG. 13A illustrates a metaplot of percent CHH methylationat all defined NRPE1 binding sites as determined by BS-seq in wild type(WT), nrpe1 and suvh2 suvh9. FIG. 13B illustrates box plots showing DNAmethylation in each cytosine context at defined NRPE1 binding sites inWT and met1. FIG. 13C illustrates that Pol V occupancy in met1 isreduced at NRPE1 sites. FIG. 13D illustrates a metaplot of DNAmethylation at sites defined as hyper-methylated in med. FIG. 13Eillustrates Pol V occupancy in met1 is increased at definedhyper-methylated sites.

FIG. 14A-FIG. 14B illustrate that tethered SUVH2 recruits Pol V throughDRD1, resulting in DNA methylation and a late-flowering phenotype. FIG.14A illustrates percent methylation at each cytosine in the FWA repeatregion as determined by BS-seq in T2 and T3 ZF-SUVH2/fwa-4 plantscompared to T2 ZF-KYP/fwa-4 (unmethylated) and WT (standard methylationpattern). ZF binding sites are shown in green and the FWA gene in blue.FIG. 14B illustrates results of a pull-down of DRD1-Flag with ZF-SUVH2.Input: DRD1-Flag extract from Arabidopsis; Beads-mock: elution fromDRD1-Flag pull-down using HAmagnetic beads pre-bound with Nicotianabenthamiana extract; Beads-ZFSUVH2: elution from DRD1-Flag pull-downusing HA-magnetic beads prebound with Nicotiana benthamiana ZF-SUVH2extract. Top panel: Flag blot; bottom panel: HA blot.

FIG. 15A-FIG. 15C illustrate that the ZF-SUVH2 construct stably recruitsPol V to FWA through a direct interaction with DRD1. FIG. 15Aillustrates Flag-ChIP in WT versus ZF-KYP (flag-tagged) showingenrichment at FWA in both the promoter and transcript region. FIG. 15Billustrates BS-Seq of FWA from a Basta-resistant line containing theZF-SUVH2 transgene and two Basta-sensitive siblings which had lost theZF-SUVH2 transgene. FIG. 15C illustrates a pull-down of HA-SUVH2 inArabidopsis using Flag-DRD1. Left panels are inputs from the twoparental strains (expressing either HA-SUVH2 (HA-2) or Flag-DRD1(Flag-D)) and the F2 line expressing both HA-SUVH2 and Flag DRD1(HA-2×Flag-d). The right panels show elution off Flag-magnetic beads.Top panels are HA blots, bottom panels are Flag blots.

FIG. 16 illustrates a list of proteins identified by DRD1immunoprecipitation-mass spectrometry.

FIG. 17 illustrates CG, CHG, and CHH methylation at the FWA gene inwild-type, fwa-4 and DMS3-ZF and MORC6-ZF early flowering lines. Redcolor represents CHH methylation, where H is C, A or T. Green colorrepresents CG methylation. Blue color represents CHG methylation. Lightblue color represents Pol V binding in wild-type compared to a polVmutant showing PolV binding to the promoter region of FWA in wild-typeplants. A schematic representation of the FWA gene is represented indark blue at the bottom.

FIG. 18 illustrates small RNAs present at the APETALA1 (At1g69120)promoter region in wild type plants (top half) or the TAL-SHH1containing plants (bottom half). SiRNAs on the top strand are in red andsiRNAs on the bottom strand are in blue.

FIG. 19 illustrates CHH DNA methylation at the SUPERMAN gene (At3g23130)promoter region in F1 plants containing only TAL-SUVH2, TAL-SHH1, orboth TAL-SHH1 and TAL-SUVH2 (TAL-SHH1/TAL-SUVH2).

DETAILED DESCRIPTION Overview

The following description is presented to enable a person of ordinaryskill in the art to make and use the various embodiments. Descriptionsof specific devices, techniques, methods, and applications are providedonly as examples. Various modifications to the examples described hereinwill be readily apparent to those of ordinary skill in the art, and thegeneral principles defined herein may be applied to other examples andapplications without departing from the spirit and scope of the variousembodiments. Thus, the various embodiments are not intended to belimited to the examples described herein and shown.

The present disclosure relates to recombinant proteins that induceepigenetic gene silencing and to methods of using such proteins forreducing the expression of genes in plants.

In Arabidopsis, DNA methylation is established by a protein called DRM2and is targeted by 24 nt small interfering RNAs (siRNAs) through apathway termed RNA-directed DNA methylation (RdDM) that involves twoplant-specific RNA polymerases: RNA Polymerase IV (Pol IV), whichfunctions to initiate siRNA biogenesis; and RNA Polymerase V (Pol V),which functions in the downstream DNA methyltransferase targeting phaseof the RdDM pathway to generate non-coding scaffold transcripts thatrecruit downstream RdDM factors. Thus, RNA-directed DNA methylation(RdDM) in Arabidopsis involves both the synthesis of non-coding,small-interfering RNAs by Pol IV and the synthesis of non-codingscaffold RNAs by Pol V.

The present disclosure is based, at least in part, on Applicant'sdiscovery that a protein called SHH1 acts in the RdDM pathway to enablesiRNA production from RdDM targets and that SHH1 is required for RNApolymerase IV (Pol IV) occupancy at these target loci. The presentdisclosure is further based, at least in part, on Applicant's discoverythat Pol V association with chromatin is dependent on two proteinscalled SUVH2 and SUVH9. Moreover, a modified SHH1, SUVH2, and/or SUVH9protein can be engineered to specifically bind different DNA sequencesby introducing a heterologous DNA-binding domain into the protein or afragment of the protein, such as a heterologous zinc finger domain orTAL effector targeting domain. Advantageously, such recombinant proteinscan be used to recruit Pol IV (for SHH1-like proteins) or Pol V (forSUVH2-like proteins and/or SUVH9-like proteins) to target loci to induceRNA-directed DNA methylation at the target loci, and thus to silence thetarget loci.

Other proteins useful in the methods of the present disclosure fortargeting Pol V, DNA methylation, and gene silencing to specific lociinclude any one of a modified DMS3, MORC6, and/or SUVR2 protein, whichcan also be engineered to specifically bind different DNA sequences byintroducing a heterologous DNA-binding domain into the protein or afragment of the protein, such as a heterologous zinc finger domain orTAL effector targeting domain.

Accordingly, the present disclosure provides methods for silencingspecific loci in plants using one or more of an SHH1 protein, a SUVH2protein, a SUVH9 protein, a DMS3 protein, a MORC6 protein, and/or aSUVR2 protein that have been engineered to specifically bind differentDNA sequences via the introduction of a heterologous DNA-binding domaininto the protein. Each one of the aforementioned modified proteins maybe expressed in a host cell individually or in various combinations toact to silence a target locus. For example, a modified SHH1 proteinhaving a heterologous DNA-binding domain may be expressed in a host cellto target Pol IV to a target locus in conjunction with one or more of amodified SUVH2 protein, SUVH9 protein, DMS3 protein, MORC6 protein,and/or SUVR2 protein having a heterologous DNA-binding domain to targetPol V to that same target locus to trigger RNA-directed DNA methylationand epigenetic silencing of that target locus.

Other proteins that may be useful for silencing specific loci in plantsaccording to the methods of the present disclosure include additionalproteins involved in RNA-directed DNA methylation. For example, othersuitable proteins for use in the methods of the present disclosure mayinclude, for example, any one of DRD1, RDM1, DRM3, DRM2, and FRG.Accordingly, the present disclosure also provides methods for silencingspecific loci in plants using one or more of an SHH1 protein, a SUVH2protein, a SUVH9 protein, a DMS3 protein, a MORC6 protein, a SUVR2protein, a DRD1 protein, an RDM1 protein, a DRM3 protein, a DRM2protein, and/or an FRG protein that have been engineered to specificallybind different DNA sequences via the introduction of a heterologousDNA-binding domain into the protein. Each one of the aforementionedmodified proteins may be expressed in a host cell individually or invarious combinations to act to silence a target locus.

The methods of the present disclosure for silencing target loci in hostcells may also involve the introduction of small interfering RNAs(siRNAs) at a target locus in conjunction with Pol V targeting by one ormore of a SUVH2 protein, a SUVH9 protein, a DMS3 protein, a MORC6protein, a SUVR2 protein, a DRD1 protein, an RDM1 protein, a DRM3protein, a DRM2 protein, and/or an FRG protein at that locus. Methods ofgenerating siRNAs are well-known in the art. These methods include, forexample, expression of hairpin RNAs that are naturally processed intosmall interfering RNAs in cells. Hairpin constructs that make smallinterfering RNAs are known in the art (EMBO Reports, 2006 November;7(11):1168-75). Additional methods for generating siRNAs include, forexample, the direct introduction of small interfering RNAs into a cellfrom exogenous sources. Methods describing bombardment of siRNAs intoplants are known in the art (Science 328, 912 (2010)). RNA molecules mayalso be sprayed (exogenous application) onto a plant so that small RNAscan then be generated in a plant cell (See U.S. Patent Application2014/0018241). Accordingly, the methods of the present disclosure forsilencing target loci in host cells may also involve the introduction ofsmall interfering RNAs (siRNAs) at a target locus in conjunction withPol V targeting by one or more of a heterologous DNA-binding domaincontaining SUVH2 protein, SUVH9 protein, DMS3 protein, MORC6 protein,SUVR2 protein, DRD1 protein, RDM1 protein, DRM3 protein, DRM2 protein,and/or FRG protein at that locus.

Silencing induced by targeting various recombinant proteins of thepresent disclosure such as, for example, SHH1-like proteins, SUVH2-likeproteins, SUVH9-like proteins, DMS3-like proteins, MORC6-like proteins,SUVR2-like proteins, DRD1-like proteins, RDM1 like proteins, DRM3-likeproteins, DRM2-like proteins, and/or FRG-like proteins, can be stable inplants even in the absence of these recombinant proteins. Accordingly,the methods of the present disclosure may allow one or more targetnucleic acids in a plant to remain silenced after the recombinantpolynucleotides of the present disclosure have been crossed out of theplant. For example, after targeting a particular region with siRNAstogether with a recombinant protein of the present disclosure thatrecruits Pol V, the silencing and DNA methylation of the targeted regionmay remain stable even after crossing away the transgenes. It is anobject of the present disclosure to provide plants having reducedexpression of one or more target nucleic acids according to the methodsof the present disclosure. As the methods of the present disclosure mayallow one or more target nucleic acids in a plant to remain silencedafter the recombinant polynucleotides of the present disclosure havebeen crossed out of the plant, the progeny plants of these plants mayhave reduced expression of one or more target nucleic acids even in theabsence of the recombinant polynucleotides that produce the recombinantpolypeptides of the present disclosure.

Definitions

Unless defined otherwise, all scientific and technical terms areunderstood to have the same meaning as commonly used in the art to whichthey pertain. For the purpose of the present disclosure, the followingterms are defined.

As used herein, a “target nucleic acid” refers to a portion ofdouble-stranded polynucleotide acid, e.g., RNA, DNA, PNA (peptidenucleic acid) or combinations thereof, to which it is advantageous tobind a protein. In one embodiment, a “target nucleic acid” is all orpart of a transcriptional control element for a gene for which a desiredphenotypic result can be attained by altering the degree of itsexpression. A transcriptional control element includes positive andnegative control elements such as a promoter, an enhancer, otherresponse elements, e.g., steroid response element, heat shock responseelement, metal response element, a repressor binding site, operator,and/or a silencer. The transcriptional control element can be viral,eukaryotic, or prokaryotic. A “target nucleic acid” also includes all ora portion of the coding region or a protein-coding gene. A “targetnucleic acid” also includes a downstream nucleic acid that can bind aprotein and whose expression is thereby modulated, typically preventingtranscription.

As used herein, a “target gene” refers to a gene whose expression is tobe reduced by a protein, such as, for example, an SHH1-like protein, aSUVH2-like protein, a SUVH9-like protein, a DMS3-like protein, aMORC6-like protein, a SUVR2-like protein, a DRD1-like protein, anRDM1-like protein, a DRM3-like protein, a DRM2-like protein, and/or anFRG-like protein.

As used herein, the terms “polynucleotide”, “nucleic acid”, “nucleicacid sequence”, “sequence of nucleic acids”, and variations thereofshall be generic to polydeoxyribonucleotides (containing2-deoxy-D-ribose), to polyribonucleotides (containing D-ribose), to anyother type of polynucleotide that is an N-glycoside of a purine orpyrimidine base, and to other polymers containing non-nucleotidicbackbones, provided that the polymers contain nucleobases in aconfiguration that allows for base pairing and base stacking, as foundin DNA and RNA. Thus, these terms include known types of nucleic acidsequence modifications, for example, substitution of one or more of thenaturally occurring nucleotides with an analog; inter-nucleotidemodifications, such as, for example, those with uncharged linkages(e.g., methyl phosphonates, phosphotriesters, phosphoramidates,carbamates, etc.), with negatively charged linkages (e.g.,phosphorothioates, phosphorodithioates, etc.), and with positivelycharged linkages (e.g., aminoalkylphosphoramidates,aminoalkylphosphotriesters); those containing pendant moieties, such as,for example, proteins (including nucleases, toxins, antibodies, signalpeptides, poly-L-lysine, etc.); those with intercalators (e.g.,acridine, psoralen, etc.); and those containing chelators (e.g., metals,radioactive metals, boron, oxidative metals, etc.). As used herein, thesymbols for nucleotides and polynucleotides are those recommended by theIUPAC-IUB Commission of Biochemical Nomenclature (Biochem. 9:4022,1970).

As used herein, a “polypeptide” is an amino acid sequence containing aplurality of consecutive polymerized amino acid residues (e.g.,optionally at least about 15 consecutive polymerized amino acidresidues, at least about 30 consecutive polymerized amino acid residues,or at least about 50 consecutive polymerized amino acid residues). Inmany instances, a polypeptide contains a polymerized amino acid residuesequence that is an enzyme, a methyltransferase, a demethylase, adeacteylase, a predicted protein of unknown function, or a domain orportion or fragment thereof. The polypeptide optionally containsmodified amino acid residues, naturally occurring amino acid residuesnot encoded by a codon, and non-naturally occurring amino acid residues.

As used herein, “protein” refers to an amino acid sequence,oligopeptide, peptide, polypeptide, or portions thereof whethernaturally occurring or synthetic.

Genes and proteins that may be used in the present disclosure includegenes encoding conservatively modified variants and proteins that areconservatively modified variants of those genes and proteins describedthroughout the application. “Conservatively modified variants” as usedherein include individual substitutions, deletions or additions to apolypeptide sequence which result in the substitution of an amino acidwith a chemically similar amino acid. Conservative substitution tablesproviding functionally similar amino acids are well known in the art.Such conservatively modified variants are in addition to and do notexclude polymorphic variants, interspecies homologs, and alleles of thedisclosure. The following eight groups contain amino acids that areconservative substitutions for one another: 1) Alanine (A), Glycine (G);2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine(Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L),Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y),Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C),Methionine (M) (see, e.g., Creighton, Proteins (1984)).

Homologs of the genes and proteins described herein may also be used inthe present disclosure. As used herein, “homology” refers to sequencesimilarity between a reference sequence and at least a fragment of asecond sequence. Homologs may be identified by any method known in theart, preferably, by using the BLAST tool to compare a reference sequenceto a single second sequence or fragment of a sequence or to a databaseof sequences. As described below, BLAST will compare sequences basedupon percent identity and similarity. As used herein, “orthology” refersto genes in different species that derive from a common ancestor gene.

The terms “identical” or percent “identity,” in the context of two ormore nucleic acids or polypeptide sequences, refer to two or moresequences or subsequences that are the same. Two sequences are“substantially identical” if two sequences have a specified percentageof amino acid residues or nucleotides that are the same (i.e., 29%identity, optionally 30%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 99% or 100% identity over a specified region, or, whennot specified, over the entire sequence), when compared and aligned formaximum correspondence over a comparison window, or designated region asmeasured using one of the following sequence comparison algorithms or bymanual alignment and visual inspection. Optionally, the identity existsover a region that is at least about 50 nucleotides (or 10 amino acids)in length, or more preferably over a region that is 100 to 500 or 1000or more nucleotides (or 20, 50, 200, or more amino acids) in length.

For sequence comparison, typically one sequence acts as a referencesequence, to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are entered into acomputer, subsequence coordinates are designated, if necessary, andsequence algorithm program parameters are designated. Default programparameters can be used, or alternative parameters can be designated. Thesequence comparison algorithm then calculates the percent sequenceidentities for the test sequences relative to the reference sequence,based on the program parameters. When comparing two sequences foridentity, it is not necessary that the sequences be contiguous, but anygap would carry with it a penalty that would reduce the overall percentidentity. For blastn, the default parameters are Gap opening penalty=5and Gap extension penalty=2. For blastp, the default parameters are Gapopening penalty=11 and Gap extension penalty=1.

A “comparison window,” as used herein, includes reference to a segmentof any one of the number of contiguous positions including, but notlimited to from 20 to 600, usually about 50 to about 200, more usuallyabout 100 to about 150 in which a sequence may be compared to areference sequence of the same number of contiguous positions after thetwo sequences are optimally aligned. Methods of alignment of sequencesfor comparison are well known in the art. Optimal alignment of sequencesfor comparison can be conducted, e.g., by the local homology algorithmof Smith and Waterman (1981), by the homology alignment algorithm ofNeedleman and Wunsch (1970) J Mol Biol 48(3):443-453, by the search forsimilarity method of Pearson and Lipman (1988) Proc Natl Acad Sci USA85(8):2444-2448, by computerized implementations of these algorithms(GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics SoftwarePackage, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or bymanual alignment and visual inspection [see, e.g., Brent et al., (2003)Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (RingbouEd)].

Two examples of algorithms that are suitable for determining percentsequence identity and sequence similarity are the BLAST and BLAST 2.0algorithms, which are described in Altschul et al. (1997) Nucleic AcidsRes 25(17):3389-3402 and Altschul et al. (1990) J. Mol Biol215(3)-403-410, respectively. Software for performing BLAST analyses ispublicly available through the National Center for BiotechnologyInformation. This algorithm involves first identifying high scoringsequence pairs (HSPs) by identifying short words of length W in thequery sequence, which either match or satisfy some positive-valuedthreshold score T when aligned with a word of the same length in adatabase sequence. T is referred to as the neighborhood word scorethreshold (Altschul et al., supra). These initial neighborhood word hitsact as seeds for initiating searches to find longer HSPs containingthem. The word hits are extended in both directions along each sequencefor as far as the cumulative alignment score can be increased.Cumulative scores are calculated using, for nucleotide sequences, theparameters M (reward score for a pair of matching residues; always >0)and N (penalty score for mismatching residues; always <0). For aminoacid sequences, a scoring matrix is used to calculate the cumulativescore. Extension of the word hits in each direction are halted when: thecumulative alignment score falls off by the quantity X from its maximumachieved value; the cumulative score goes to zero or below, due to theaccumulation of one or more negative-scoring residue alignments; or theend of either sequence is reached. The BLAST algorithm parameters W, T,and X determine the sensitivity and speed of the alignment. The BLASTNprogram (for nucleotide sequences) uses as defaults a wordlength (W) of11, an expectation (E) or 10, M=5, N=−4, and a comparison of bothstrands. For amino acid sequences, the BLASTP program uses as defaults awordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoringmatrix (see Henikoff and Henikoff, (1992) Proc Natl Acad Sci USA89(22):10915-10919) alignments (B) of 50, expectation (E) of 10, M=5,N=−4, and a comparison of both strands.

The BLAST algorithm also performs a statistical analysis of thesimilarity between two sequences (see, e.g., Karlin and Altschul, (1993)Proc Natl Acad Sci USA 90(12):5873-5877). One measure of similarityprovided by the BLAST algorithm is the smallest sum probability (P(N)),which provides an indication of the probability by which a match betweentwo nucleotide or amino acid sequences would occur by chance. Forexample, a nucleic acid is considered similar to a reference sequence ifthe smallest sum probability in a comparison of the test nucleic acid tothe reference nucleic acid is less than about 0.2, more preferably lessthan about 0.01, and most preferably less than about 0.001.

Other than percentage of sequence identity noted above, anotherindication that two nucleic acid sequences or polypeptides aresubstantially identical is that the polypeptide encoded by the firstnucleic acid is immunologically cross-reactive with the antibodiesraised against the polypeptide encoded by the second nucleic acid. Thus,a polypeptide is typically substantially identical to a secondpolypeptide, for example, where the two peptides differ only byconservative substitutions. Another indication that two nucleic acidsequences are substantially identical is that the two molecules or theircomplements hybridize to each other under stringent conditions. Yetanother indication that two nucleic acid sequences are substantiallyidentical is that the same primers can be used to amplify the sequence.

Recombinant Proteins of the Present Disclosure

Provided herein are recombinant proteins for use in reducing theexpression of a target nucleic acid in a plant. In some embodiments, arecombinant protein of the present disclosure interacts with an RNApolymerase. This interaction may be direct or it may be indirect.Whether the interaction of a recombinant protein of the presentdisclosure with an RNA polymerase is direct or indirect, the interactionfacilitates the recruitment of the RNA polymerase to a nucleic acid. Insome embodiments, one or more additional proteins may be furtherinvolved in facilitating the interaction of a recombinant protein of thepresent disclosure with an RNA polymerase and recruitment of the RNApolymerase to a nucleic acid. In some embodiments, an SHH1-like proteininteracts, directly or indirectly, with RNA Pol IV and this interactionfacilitates the recruitment of RNA Pol IV to a nucleic acid. In someembodiments, a SUVH2-like protein and/or a SUVH9-like protein interacts,directly or indirectly, with RNA Pol V and this interaction facilitatesthe recruitment of RNA Pol V to a nucleic acid. In some embodiments,DMS3-like proteins, MORC6-like proteins, and/or SUVR2-like proteinsinteract, directly or indirectly, with RNA Pol V and this interactionfacilitates the recruitment of RNA Pol V to a nucleic acid. In someembodiments, DMS3-like proteins, MORC6-like proteins, SUVR2-likeproteins, DRD1-like proteins, RDM1 like proteins, DRM3-like proteins,DRM2-like proteins, and/or FRG-like proteins, interact, directly orindirectly, with RNA Pol V and this interaction facilitates therecruitment of RNA Pol V to a nucleic acid. In some embodiments, therecombinant proteins of the present disclosure facilitate RNA-directedDNA methylation of a nucleic acid.

In some embodiments, SHH1-like proteins, SUVH2-like proteins, SUVH9-likeproteins, DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins,DRD1-like proteins, RDM1-like proteins, DRM3-like proteins, DRM2-likeproteins, and/or FRG-like proteins are targeted to the same nucleic acidand cooperatively act to silence the expression of the target nucleicacid. Recombinant proteins of the present disclosure, for exampleSHH1-like proteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-likeproteins, MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins,RDM1 like proteins, DRM3-like proteins, DRM2-like proteins, and/orFRG-like proteins may be recombinantly expressed in a cell either aloneor in combinations.

SHH1 Proteins

Certain aspects of the present disclosure relate to SHH1-like proteins.In some embodiments, an SHH1-like protein refers to a recombinant SHH1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. SHH1-like proteins may be used in reducing the expression of oneor more target nucleic acids, such as genes, in plants.

SHH1 proteins of the present disclosure are SAWADEE HOMEODOMAIN HOMOLOG1 (SHH1) proteins. Full-length SHH1 proteins contain a chromatin-bindingSAWADEE domain. The SAWADEE chromatin-binding domain adopts a uniquetandem Tudor-like fold and functions as a dual lysine reader, probingfor both unmethylated K4 and methylated K9 modifications on the histone3 (H3) tail. SHH1 proteins also contain a homeodomain. In someembodiments, SHH1-like proteins of the present disclosure arechromatin-binding proteins.

In some embodiments, an SHH1-like protein of the present disclosureincludes a functional fragment of a full-length SHH1 protein where thefragment maintains the ability to recruit RNA Pol IV to DNA. In someembodiments, an SHH1 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length SHH1 protein. In some embodiments, SHH1 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length SHH1 protein. In someembodiments, SHH1 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length SHH1 protein. In someembodiments, SHH1 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length SHH1 protein.

Suitable SHH1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SHH1 proteins may include, for example, thoselisted in Table 1, homologs thereof, and orthologs thereof.

TABLE 1 SHH1 Proteins Organism Gene Name SED ID NO. Arabidopsis thalianaNP_849666.2 1 Ricinus communis XP_002515974.1 2 Glycine maxXP_003531650.1 3 Zea mays NP_001141052.1 4 Medicago truncatulaAFK39040.1 5 Physcomitrella patens XP_001760710.1 6 Sorghum bicolorXP_002462170.1 7 Oryza sativa NP_001062942.1 8 Brachypodium distachyonXP_003563870.1 9 Populus trichocarpa XP_002299736.1 10 Vitis viniferaXP_002283948.1 11 Cucumis sativus XP_004155951.1 12 Arabidopsis lyrataXP_002890094.1 13 Arabidopsis thaliana AEE76089 40

In some embodiments, an SHH1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SHH1 protein (i.e., SEQ ID NO: 1).

In some embodiments, the homolog of an SHH1 protein, or the homolog of afragment of an SHH1 protein, is the amino acid sequence of theArabidopsis thaliana SHH2 protein (SEQ ID NO: 40).

An SHH1-like protein may include the amino acid sequence or a fragmentthereof of any SHH1 homolog or ortholog, such as any one of those listedin Table 1. One of skill would readily recognize that additional SHH1homologs and/or orthologs may exist and may be used herein.

SUVH2 Proteins and SUVH9 Proteins

Certain aspects of the present disclosure relate to SUVH2-like proteinsand SUVH9-like proteins. In some embodiments, a SUVH2-like proteinrefers to a recombinant SUVH2 protein or fragment thereof and thatcontains a heterologous DNA-binding domain. In some embodiments, aSUVH9-like protein refers to a recombinant SUVH9 protein or fragmentthereof and that contains a heterologous DNA-binding domain. SUVH2-likeproteins and/or SUVH9-like proteins may be used in reducing theexpression of one or more target nucleic acids, such as genes, inplants.

SUVH2 and SUVH9 proteins of the present disclosure are SU-VAR(3-9)Homologs. Full-length SUVH2 and SUVH9 proteins contain a two-helixbundle domain towards the N-terminus, a SRA domain, and the pre-SET andSET domains towards the C-terminus. The structural and sequence featuresof the SUVH domains are known in the art and are provided herein. Insome embodiments, SUVH2-like proteins and/or SUVH9-like proteins of thepresent disclosure may contain one or more of the canonical SUVH domainsincluding a two-helix bundle domain, a SRA domain, a pre-SET domain,and/or a SET domain.

In some embodiments, a SUVH2-like protein of the present disclosureincludes a functional fragment of a full-length SUVH2 protein where thefragment maintains the ability to recruit RNA Pol V to DNA. In someembodiments, a SUVH2 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, at least 260 consecutive amino acids, atleast 280 consecutive amino acids, at least 300 consecutive amino acids,at least 325 consecutive amino acids, at least 350 consecutive aminoacids, at least 375 consecutive amino acids, at least 400 consecutiveamino acids, at least 425 consecutive amino acids, at least 450consecutive amino acids, at least 475 consecutive amino acids, at least500 consecutive amino acids, at least 525 consecutive amino acids, atleast 550 consecutive amino acids, at least 575 consecutive amino acids,at least 600 consecutive amino acids, at least 625 consecutive aminoacids, or 626 or more consecutive amino acids of a full-length SUVH2protein. In some embodiments, SUVH2 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length SUVH2 protein. In some embodiments,SUVH2 protein fragments may include sequences with one or more aminoacids replaced/substituted with an amino acid different from theendogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length SUVH2 protein. In someembodiments, SUVH2 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length SUVH2 protein.

Suitable SUVH2 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SUVH2 proteins may include, for example, thoselisted in Table 2, homologs thereof, and orthologs thereof.

TABLE 2 SUVH2 Proteins Organism Gene Name SEQ ID NO. Arabidopsisthaliana NP_180887.1 14 Ricinus communis XP_002528332.1 15 Glycine maxXP_003530311.1 16 Zea mays DAA60407.1 17 Medicago truncatulaXP_003619209.1 18 Physcomitrella patens XP_001753516.1 19 Sorghumbicolor XP_002459773.1 20 Oryza sativa EAZ03669.1 21 Brachypodiumdistachyon XP_003563196.1 22 Populus trichocarpa XP_002315593.1 23 Vitisvinifera XP_002282386.1 24 Cucumis sativus XP_004134031.1 25 Arabidopsislyrata XP_002879445.1 26

In some embodiments, a SUVH2 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SUVH2 protein (i.e., SEQ ID NO: 14).

A SUVH2-like protein may include the amino acid sequence or a fragmentthereof of any SUVH2 homolog or ortholog, such as any one of thoselisted in Table 2. One of skill would readily recognize that additionalSUVH2 homologs and/or orthologs may exist and may be used herein.

In some embodiments, a SUVH9-like protein of the present disclosureincludes a functional fragment of a full-length SUVH9 protein where thefragment maintains the ability to recruit RNA Pol V to DNA. In someembodiments, a SUVH9 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, at least 260 consecutive amino acids, atleast 280 consecutive amino acids, at least 300 consecutive amino acids,at least 325 consecutive amino acids, at least 350 consecutive aminoacids, at least 375 consecutive amino acids, at least 400 consecutiveamino acids, at least 425 consecutive amino acids, at least 450consecutive amino acids, at least 475 consecutive amino acids, at least500 consecutive amino acids, at least 525 consecutive amino acids, atleast 550 consecutive amino acids, at least 575 consecutive amino acids,at least 600 consecutive amino acids, at least 625 consecutive aminoacids, or 626 or more consecutive amino acids of a full-length SUVH9protein. In some embodiments, SUVH9 protein fragments may includesequences with one or more amino acids removed from the consecutiveamino acid sequence of a full-length SUVH9 protein. In some embodiments,SUVH9 protein fragments may include sequences with one or more aminoacids replaced/substituted with an amino acid different from theendogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length SUVH9 protein. In someembodiments, SUVH9 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length SUVH9 protein.

Suitable SUVH9 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SUVH9 proteins may include, for example, thoselisted in Table 3, homologs thereof, and orthologs thereof.

TABLE 3 SUVH9 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana AF344452.1 27 Ricinus communis XP_002528332.1 28 Glycine maxXP_003530311.1 29 Zea mays DAA60407.1 30 Medicago truncatulaXP_003619209.1 31 Physcomitrella patens XP_001753516.1 32 Sorghumbicolor XP_002459773.1 33 Oryza sativa EAZ03669.1 34 Brachypodiumdistachyon XP_003563196.1 35 Populus trichocarpa XP_002315593.1 36 Vitisvinifera XP_002282386.1 37 Cucumis sativus XP_004134031.1 38 Arabidopsislyrata XP_002863127.1 39

In some embodiments, a SUVH9 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SUVH9 protein (i.e., SEQ ID NO: 27).

A SUVH9-like protein may include the amino acid sequence or a fragmentthereof of any SUVH9 homolog or ortholog, such as any one of thoselisted in Table 3. One of skill would readily recognize that additionalSUVH9 homologs and/or orthologs may exist and may be used herein.

DMS3 Proteins

Certain aspects of the present disclosure relate to DMS3-like proteins.In some embodiments, a DMS3-like protein refers to a recombinant DMS3protein or fragment thereof and that contains a heterologous DNA-bindingdomain. DMS3-like proteins may be used in reducing the expression of oneor more target nucleic acids, such as genes, in plants.

DMS3 proteins are known in the art and are described herein. In someembodiments, a DMS3-like protein of the present disclosure includes afunctional fragment of a full-length DMS3 protein where the fragmentmaintains one or more functions of the full-length protein. In someembodiments, a DMS3 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DMS3 protein. In some embodiments, DMS3 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length DMS3 protein. In someembodiments, DMS3 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length DMS3 protein. In someembodiments, DMS3 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length DMS3 protein.

Suitable DMS3 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable DMS3 proteins may include, for example, thoselisted in Table 4, homologs thereof, and orthologs thereof.

TABLE 4 DMS3 Proteins Organism Gene Name SEQ ID NO: Arabidopsis thalianaDMS3 41 Solanum lycopersicum XP_004234924.1 42 Solanum tuberosumXP_006350630.1 43 Phaseolus vulgaris ESW19314.1 44 Vitis viniferaXP_002277586.1 45 Theobroma cacao EOY23566.1 46 Glycine maxXP_003550866.1 47 Oriza sativa Japonica group NP_001042520.1 48 Orizasativa Indica group EEC70256.1 49 Zea mays NP_001132336.1 50 Sorghumbicolor XP_002454876.1 51

In some embodiments, a DMS3 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana DMS3 protein (i.e., SEQ ID NO: 41).

In some embodiments, the homolog of a DMS3 protein, or the homolog of afragment of a DMS3 protein, may also be used in the methods of thepresent disclosure.

A DMS3-like protein may include the amino acid sequence or a fragmentthereof of any DMS3 homolog or ortholog, such as, for example, any oneof those listed in Table 4. One of skill would readily recognize thatadditional DMS3 homologs and/or orthologs may exist and may be usedherein.

MORC6 Proteins

Certain aspects of the present disclosure relate to MORC6-like proteins.In some embodiments, a MORC6-like protein refers to a recombinant MORC6protein or fragment thereof and that contains a heterologous DNA-bindingdomain. MORC6-like proteins may be used in reducing the expression ofone or more target nucleic acids, such as genes, in plants.

MORC6 proteins are known in the art and are described herein. In someembodiments, a MORC6-like protein of the present disclosure includes afunctional fragment of a full-length MORC6 protein where the fragmentmaintains one or more functions of the full-length protein. In someembodiments, a MORC6 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length MORC6 protein. In some embodiments, MORC6 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length MORC6 protein. In someembodiments, MORC6 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length MORC6 protein. In someembodiments, MORC6 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length MORC6 protein.

Suitable MORC6 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable MORC6 proteins may include, for example, thoselisted in Table 5, homologs thereof, and orthologs thereof.

TABLE 5 MORC6 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana MORC6 53 Solanum lycopersicum XP_004230214.1 54 Solanumtuberosum XP_006344837.1 55 Phaseolus vulgaris ESW10038.1 56 Vitisvinifera XP_002278685.1 57 Theobroma cacao EOY20772.1 58 Triticum urarteEMS64080.1 59 Glycine max XP_003523086.1 60 Oriza sativa Japonica groupEEE54777.1 61 Oriza sativa Indica group EEC70857.1 62 Zea maysAFW84846.1 63 Sorghum bicolor XP_002455787.1 64

In some embodiments, a MORC6 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana MORC6 protein (i.e., SEQ ID NO: 53).

In some embodiments, the homolog of a MORC6 protein, or the homolog of afragment of a MORC6 protein, may also be used in the methods of thepresent disclosure.

A MORC6-like protein may include the amino acid sequence or a fragmentthereof of any MORC6 homolog or ortholog, such as, for example, any oneof those listed in Table 5. One of skill would readily recognize thatadditional MORC6 homologs and/or orthologs may exist and may be usedherein.

SUVR2 Proteins

Certain aspects of the present disclosure relate to SUVR2-like proteins.In some embodiments, a SUVR2-like protein refers to a recombinant SUVR2protein or fragment thereof and that contains a heterologous DNA-bindingdomain. SUVR2-like proteins may be used in reducing the expression ofone or more target nucleic acids, such as genes, in plants.

SUVR2 proteins are known in the art and are described herein. In someembodiments, a SUVR2-like protein of the present disclosure includes afunctional fragment of a full-length SUVR2 protein where the fragmentmaintains one or more functions of the full-length protein. In someembodiments, a SUVR2 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length SUVR2 protein. In some embodiments, SUVR2 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length SUVR2 protein. In someembodiments, SUVR2 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length SUVR2 protein. In someembodiments, SUVR2 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length SUVR2 protein.

Suitable SUVR2 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, Medicagotruncatula, Physcomitrella patens, Sorghum bicolor, and Oryza sativa.Examples of suitable SUVR2 proteins may include, for example, thoselisted in Table 6, homologs thereof, and orthologs thereof.

TABLE 6 SUVR2 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana SUVR2 66 Solanum lycopersicum XP_004247936.1 67 Solanumtuberosum XP_006358446.1 68 Phaseolus vulgaris ESW16847.1 69 Vitisvinifera XP_002270320.2 70 Theobroma cacao EOX94338.1 71 Triticum urarteEMS67506.1 72 Glycine max XP_003541369.1 73 Oriza sativa Japonica groupNP_001047458.1 74 Oriza sativa Indica group EEC78330.1 75 Zea maysDAA48520.1 76 Sorghum bicolor XP_002445655.1 77

In some embodiments, a SUVR2 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana SUVR2 protein (i.e., SEQ ID NO: 66).

In some embodiments, the homolog of a SUVR2 protein, or the homolog of afragment of a SUVR2 protein, may also be used in the methods of thepresent disclosure.

A SUVR2-like protein may include the amino acid sequence or a fragmentthereof of any SUVR2 homolog or ortholog, such as, for example, any oneof those listed in Table 6. One of skill would readily recognize thatadditional SUVR2 homologs and/or orthologs may exist and may be usedherein.

DRD1 Proteins

Certain aspects of the present disclosure relate to DRD1-like proteins.In some embodiments, a DRD1-like protein refers to a recombinant DRD1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. DRD1-like proteins may be used in reducing the expression of oneor more target nucleic acids, such as genes, in plants.

DRD1 proteins are known in the art and are described herein. In someembodiments, a DRD1-like protein of the present disclosure includes afunctional fragment of a full-length DRD1 protein where the fragmentmaintains one or more functions of the full-length protein. In someembodiments, a DRD1 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DRD1 protein. In some embodiments, DRD1 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length DRD1 protein. In someembodiments, DRD1 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length DRD1 protein. In someembodiments, DRD1 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length DRD1 protein.

Suitable DRD1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Physcomitrella patens, Sorghum bicolor, and Oryza sativa. Examples ofsuitable DRD1 proteins may include, for example, those listed in Table7, homologs thereof, and orthologs thereof.

TABLE 7 DRD1 Proteins Organism Gene Name SEQ ID NO: Arabidopsis thalianaNP_179232.1 79 Ricinus communis XP_002530324.1 80 Glycine maxXP_003540522.1 81 Zea mays AFW57413.1 82 Physcomitrella patensXP_001752976.1 83 Sorghum bicolor XP_002445019.1 84 Oryza sativaBAC84084.1 85 Brachypodium distachyon XP_003571619.1 86 Populustrichocarpa XP_002313774.2 87 Vitis vinifera XP_002273814.1 88 Cucumissativus XP_004170971.1 89 Arabidopsis lyrata XP_002884170.1 90

In some embodiments, a DRD1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana DRD1 protein (i.e., SEQ ID NO: 79).

In some embodiments, the homolog of a DRD1 protein, or the homolog of afragment of a DRD1 protein, may also be used in the methods of thepresent disclosure.

A DRD1-like protein may include the amino acid sequence or a fragmentthereof of any DRD1 homolog or ortholog, such as, for example, any oneof those listed in Table 7. One of skill would readily recognize thatadditional DRD1 homologs and/or orthologs may exist and may be usedherein.

RDM1 Proteins

Certain aspects of the present disclosure relate to RDM1-like proteins.In some embodiments, a RDM1-like protein refers to a recombinant RDM1protein or fragment thereof and that contains a heterologous DNA-bindingdomain. RDM1-like proteins may be used in reducing the expression of oneor more target nucleic acids, such as genes, in plants.

RDM1 proteins are known in the art and are described herein. In someembodiments, a RDM1-like protein of the present disclosure includes afunctional fragment of a full-length RDM1 protein where the fragmentmaintains one or more functions of the full-length protein. In someembodiments, a RDM1 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length RDM1 protein. In some embodiments, RDM1 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length RDM1 protein. In someembodiments, RDM1 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length RDM1 protein. In someembodiments, RDM1 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length RDM1 protein.

Suitable RDM1 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays, and Oryzasativa. Examples of suitable RDM1 proteins may include, for example,those listed in Table 8, homologs thereof, and orthologs thereof.

TABLE 8 RDM1 Proteins Organism Gene Name SEQ ID NO: Arabidopsis thalianaNP_188907.2 91 Ricinus communis XP_002517093.1 92 Glycine maxNP_001237231.1 93 Zea mays NP_001170520.1 94 Medicago truncatulaXP_003610752.1 95 Oryza sativa BAD38576.1 96 Populus trichocarpaXP_002311634.1 97 Vitis vinifera XP_002279112.2 98 Cucumis sativusXP_004134127.1 99 Arabidopsis lyrata XP_002883375.1 100

In some embodiments, a RDM1 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana RDM1 protein (i.e., SEQ ID NO: 91).

In some embodiments, the homolog of a RDM1 protein, or the homolog of afragment of a RDM1 protein, may also be used in the methods of thepresent disclosure.

A RDM1-like protein may include the amino acid sequence or a fragmentthereof of any RDM1 homolog or ortholog, such as, for example, any oneof those listed in Table 8. One of skill would readily recognize thatadditional RDM1 homologs and/or orthologs may exist and may be usedherein.

DRM3 Proteins

Certain aspects of the present disclosure relate to DRM3-like proteins.In some embodiments, a DRM3-like protein refers to a recombinant DRM3protein or fragment thereof and that contains a heterologous DNA-bindingdomain. DRM3-like proteins may be used in reducing the expression of oneor more target nucleic acids, such as genes, in plants.

DRM3 proteins are known in the art and are described herein. In someembodiments, a DRM3-like protein of the present disclosure includes afunctional fragment of a full-length DRM3 protein where the fragmentmaintains one or more functions of the full-length protein. In someembodiments, a DRM3 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DRM3 protein. In some embodiments, DRM3 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length DRM3 protein. In someembodiments, DRM3 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length DRM3 protein. In someembodiments, DRM3 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length DRM3 protein.

Suitable DRM3 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Physcomitrella patens, Sorghum bicolor, and Oryza sativa. Examples ofsuitable DRM3 proteins may include, for example, those listed in Table9, homologs thereof, and orthologs thereof.

TABLE 9 DRM3 Proteins Organism Gene Name SEQ ID NO: Arabidopsis thalianaNP_566573.1 101 Ricinus communis XP_002519294.1 102 Glycine maxXP_006583974.1 103 Zea mays NP_001105094.1 104 Medicago truncatulaXP_003609841.1 105 Sorghum bicolor XP_002468285.1 106 Oryza sativaAAT85176.1 107 Brachypodium distachyon XP_003569077.1 108 Populustrichocarpa XP_002316067.2 109 Vitis vinifera XP_002264226.1 110 Cucumissativus XP_004138523.1 111 Arabidopsis lyrata XP_002885200.1 112

In some embodiments, a DRM3 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana DRM3 protein (i.e., SEQ ID NO: 101).

In some embodiments, the homolog of a DRM3 protein, or the homolog of afragment of a DRM3 protein, may also be used in the methods of thepresent disclosure.

A DRM3-like protein may include the amino acid sequence or a fragmentthereof of any DRM3 homolog or ortholog, such as, for example, any oneof those listed in Table 9. One of skill would readily recognize thatadditional DRM3 homologs and/or orthologs may exist and may be usedherein.

DRM2 Proteins

Certain aspects of the present disclosure relate to DRM2-like proteins.In some embodiments, a DRM2-like protein refers to a recombinant DRM2protein or fragment thereof and that contains a heterologous DNA-bindingdomain. DRM2-like proteins may be used in reducing the expression of oneor more target nucleic acids, such as genes, in plants.

DRM2 proteins are known in the art and are described herein. In someembodiments, a DRM2-like protein of the present disclosure includes afunctional fragment of a full-length DRM2 protein where the fragmentmaintains one or more functions of the full-length protein. In someembodiments, a DRM2 protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length DRM2 protein. In some embodiments, DRM2 protein fragmentsmay include sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length DRM2 protein. In someembodiments, DRM2 protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length DRM2 protein. In someembodiments, DRM2 protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length DRM2 protein.

Suitable DRM2 proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Physcomitrella patens, Sorghum bicolor, and Oryza sativa. Examples ofsuitable DRM2 proteins may include, for example, those listed in Table10, homologs thereof, and orthologs thereof.

TABLE 10 DRM2 Proteins Organism Gene Name SEQ ID NO: Arabidopsisthaliana NP_196966.2 113 Ricinus communis XP_002521449.1 114 Glycine maxXP_003524549.1 115 Zea mays NP_001104977.1 116 Medicago truncatulaXP_003618189.1 117 Sorghum bicolor XP_002468660.1 118 Oryza sativaABF93591.1 119 Brachypodium distachyon XP_003575456.1 120 Populustrichocarpa XP_002300046.2 121 Vitis vinifera XP_002273972.2 122 Cucumissativus XP_004141100.1 123 Arabidopsis lyrata XP_002873681.1 124

In some embodiments, a DRM2 protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana DRM2 protein (i.e., SEQ ID NO: 113).

In some embodiments, the homolog of a DRM2 protein, or the homolog of afragment of a DRM2 protein, may also be used in the methods of thepresent disclosure.

A DRM2-like protein may include the amino acid sequence or a fragmentthereof of any DRM2 homolog or ortholog, such as, for example, any oneof those listed in Table 10. One of skill would readily recognize thatadditional DRM2 homologs and/or orthologs may exist and may be usedherein.

FRG Proteins

Certain aspects of the present disclosure relate to FRG-like proteins.In some embodiments, a FRG-like protein refers to a recombinant FRGprotein or fragment thereof and that contains a heterologous DNA-bindingdomain. FRG-like proteins may be used in reducing the expression of oneor more target nucleic acids, such as genes, in plants.

FRG proteins are known in the art and are described herein. In someembodiments, a FRG-like protein of the present disclosure includes afunctional fragment of a full-length FRG protein where the fragmentmaintains one or more functions of the full-length protein. In someembodiments, a FRG protein fragment contains at least 20 consecutiveamino acids, at least 30 consecutive amino acids, at least 40consecutive amino acids, at least 50 consecutive amino acids, at least60 consecutive amino acids, at least 70 consecutive amino acids, atleast 80 consecutive amino acids, at least 90 consecutive amino acids,at least 100 consecutive amino acids, at least 120 consecutive aminoacids, at least 140 consecutive amino acids, at least 160 consecutiveamino acids, at least 180 consecutive amino acids, at least 200consecutive amino acids, at least 220 consecutive amino acids, at least240 consecutive amino acids, or 241 or more consecutive amino acids of afull-length FRG protein. In some embodiments, FRG protein fragments mayinclude sequences with one or more amino acids removed from theconsecutive amino acid sequence of a full-length FRG protein. In someembodiments, FRG protein fragments may include sequences with one ormore amino acids replaced/substituted with an amino acid different fromthe endogenous amino acid present at a given amino acid position in aconsecutive amino acid sequence of a full-length FRG protein. In someembodiments, FRG protein fragments may include sequences with one ormore amino acids added to an otherwise consecutive amino acid sequenceof a full-length FRG protein.

Suitable FRG proteins may be identified and isolated from monocot anddicot plants. Examples of such plants may include, for example,Arabidopsis spp., Ricinus communis, Glycine max, Zea Mays,Physcomitrella patens, Sorghum bicolor, and Oryza sativa. Examples ofsuitable FRG proteins may include, for example, those listed in Table11, homologs thereof, and orthologs thereof.

TABLE 11 FRG Proteins Organism Gene Name SEQ ID NO: Arabidopsis thalianaNP_188635.1 125 Ricinus communis XP_002513133.1 126 Glycine maxXP_003555190.1 127 Zea mays AFW61101.1 128 Medicago truncatulaXP_003593498.1 129 Physcomitrella patens XP_001770987.1 130 Sorghumbicolor XP_002458594.1 131 Oryza sativa NP_001061138.1 132 Brachypodiumdistachyon XP_003560909.1 133 Populus trichocarpa XP_002305010.2 134Vitis vinifera XP_002267403 135 Cucumis sativus XP_004134959 136Arabidopsis lyrata XP_002883222.1 137

In some embodiments, a FRG protein or fragment thereof of the presentdisclosure has an amino acid sequence with at least about 20%, at leastabout 25%, at least about 30%, at least about 40%, at least about 50%,at least about 55%, at least about 60%, at least about 65%, at leastabout 70%, at least about 75%, at least about 80%, at least about 85%,at least about 90%, at least about 91%, at least about 92%, at leastabout 93%, at least about 94%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 100% amino acid identity to the amino acid sequence of the A.thaliana FRG protein (i.e., SEQ ID NO: 125).

In some embodiments, the homolog of a FRG protein, or the homolog of afragment of a FRG protein, may also be used in the methods of thepresent disclosure.

A FRG-like protein may include the amino acid sequence or a fragmentthereof of any FRG homolog or ortholog, such as, for example, any one ofthose listed in Table 11. One of skill would readily recognize thatadditional FRG homologs and/or orthologs may exist and may be usedherein.

DNA-Binding Domains

SHH1-like proteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-likeproteins, MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins,RDM1-like proteins, DRM3-like proteins, DRM2-like proteins, and/orFRG-like proteins of the present disclosure have DNA-binding activity.This DNA-binding activity is achieved through a heterologous DNA-bindingdomain. In some embodiments, recombinant proteins of the presentdisclosure contain a DNA-binding domain. Recombinant proteins of thepresent disclosure may contain one DNA binding domain or they maycontain more than one DNA-binding domain.

In some embodiments, the DNA-binding domain is a zinc finger domain. Asdisclosed herein, a “zinc finger domain” refers to a DNA-binding proteindomain that contains zinc fingers, which are small protein structuralmotifs that can coordinate one or more zinc ions to help stabilize theirprotein folding. Zinc fingers can generally be classified into severaldifferent structural families and typically function as interactionmodules that bind DNA, RNA, proteins, or small molecules. Suitable zincfinger domains of the present disclosure may contain two, three, four,five, six, seven, eight, or nine zinc fingers. Examples of suitable zincfinger domains may include, for example, Cys2His2 (C2H2) zinc fingerdomains, C-x8-C-x5-C-x3-H (CCCH) zinc finger domains, multi-cysteinezinc finger domains, and zinc binuclear cluster domains.

In some embodiments, the DNA-binding domain binds a specific nucleicacid sequence. For example, the DNA-binding domain may bind a sequencethat is at least 5 nucleotides, at least 6 nucleotides, at least 7nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, atleast 20 nucleotides, at least 25 nucleotides, at least 30 nucleotides,at least 35 nucleotides, at least 40 nucleotides, at least 45nucleotides, at least 50 nucleotides, or a high number of nucleotides inlength. In some embodiments, the DNA-binding domain binds a sequencethat is 8 nucleotides in length.

In some embodiments, a recombinant protein of the present disclosurefurther contains two N-terminal CCCH zinc finger domains.

In some embodiments, the zinc finger domain is an engineered zinc fingerarray, such as a C2H2 zinc finger array. Engineered arrays of C2H2 zincfingers can be used to create DNA-binding proteins capable of targetingdesired genomic DNA sequences. Methods of engineering zinc finger arraysare well known in the art, and include, for example, combining smallerzinc fingers of known specificity.

In some embodiments, the recombinant protein may contain a DNA-bindingdomain other than a zinc finger domain. Examples of such DNA-bindingdomains may include, for example, TAL (transcription activator-like)effector targeting domains, helix-turn-helix family DNA-binding domains,basic domains, ribbon-helix-helix domains, TBP (TATA-box bindingprotein) domains, barrel dimer domains, RHB domains (real homologydomain), BAH (bromo-adjacent homology) domains, SANT domains,Chromodomains, Tudor domains, Bromodomains, PHD domains (plant homeodomain), WD40 domains, and MBD domains (methyl-CpG-binding domain).

In some embodiments, the DNA-binding domain is a TAL effector targetingdomain. As used herein, TAL effectors refer to secreted bacterialproteins, such as those secreted by Xanthomonas or Ralstonia bacteriawhen infecting various plant species. Generally, TAL effectors arecapable of binding promoter sequences in the host plant, and activatethe expression of plant genes that aid in bacterial infection. TALeffectors recognize plant DNA sequences through a central repeattargeting domain that contains a variable number of approximately 34amino acid repeats. Moreover, TAL effector targeting domains can beengineered to target specific DNA sequences. Methods of modifying TALeffector targeting domains are well known in the art, and described inBogdanove and Voytas, Science. 2011 Sep. 30; 333(6051):1843-6.

Recombinant Nucleic Acids Encoding Recombinant Proteins

Certain aspects of the present disclosure relate to recombinant nucleicacids encoding recombinant proteins that contain a heterologousDNA-binding domain. The recombinant proteins may be SHH1-like proteins,SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins, MORC6-likeproteins, SUVR2-like proteins, DRD1-like proteins, RDM1-like proteins,DRM3-like proteins, DRM2-like proteins, and/or FRG-like proteins.Examples of heterologous DNA-binding domains may include, a CCCH zincfinger domain, a multi-cysteine zinc finger domain, a zinc binuclearcluster domain, a C2H2 zinc finger domain having less than three zincfingers, a C2H2 zinc finger domain having more than three zinc fingers,a zinc finger array, a TAL effector targeting domain, a helix-turn-helixfamily DNA-binding domain, a basic domain, a ribbon-helix-helix domain,a TBP domain, a barrel dimer domain, a real homology domain, a BAHdomain, a SANT domain, a Chromodomain, a Tudor domain, a Bromodomain, aPHD domain, a WD40 domain, and a MBD domain.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SHH1-like protein, where the SHH1-like protein containsa DNA-binding domain and an SHH1 polypeptide or a fragment thereof. Insome embodiments, the SHH1 polypeptide or fragment thereof has an aminoacid sequence that is at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75% at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to SEQ ID NO: 1.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SUVH2-like protein, where the SUVH2-like proteincontains a DNA-binding domain and a SUVH2 polypeptide or a fragmentthereof. In some embodiments, the SUVH2 polypeptide or fragment thereofhas an amino acid sequence that is at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% identical to SEQ ID NO: 14.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding an SUVH9-like protein, where the SUVH9-like proteincontains a DNA-binding domain and a SUVH9 polypeptide or a fragmentthereof. In some embodiments, the SUVH9 polypeptide or fragment thereofhas an amino acid sequence that is at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% identical to SEQ ID NO: 27.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a DMS3-like protein, where the DMS3-like protein containsa DNA-binding domain and a DMS3 polypeptide or a fragment thereof. Insome embodiments, the DMS3 polypeptide or fragment thereof has an aminoacid sequence that is at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to SEQ ID NO: 41.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a MORC6-like protein, where the MORC6-like proteincontains a DNA-binding domain and a MORC6 polypeptide or a fragmentthereof. In some embodiments, the MORC6 polypeptide or fragment thereofhas an amino acid sequence that is at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% identical to SEQ ID NO: 53.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a SUVR2-like protein, where the SUVR2-like proteincontains a DNA-binding domain and a SUVR2 polypeptide or a fragmentthereof. In some embodiments, the SUVR2 polypeptide or fragment thereofhas an amino acid sequence that is at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% identical to SEQ ID NO: 66.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a DRD1-like protein, where the DRD1-like protein containsa DNA-binding domain and a DRD1 polypeptide or a fragment thereof. Insome embodiments, the DRD1 polypeptide or fragment thereof has an aminoacid sequence that is at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to SEQ ID NO: 79.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a RDM1-like protein, where the RDM1-like protein containsa DNA-binding domain and a RDM1 polypeptide or a fragment thereof. Insome embodiments, the RDM1 polypeptide or fragment thereof has an aminoacid sequence that is at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to SEQ ID NO: 91.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a DRM3-like protein, where the DRM3-like protein containsa DNA-binding domain and a DRM3 polypeptide or a fragment thereof. Insome embodiments, the DRM3 polypeptide or fragment thereof has an aminoacid sequence that is at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to SEQ ID NO: 101.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a DRM2-like protein, where the DRM2-like protein containsa DNA-binding domain and a DRM2 polypeptide or a fragment thereof. Insome embodiments, the DRM2 polypeptide or fragment thereof has an aminoacid sequence that is at least 50%, at least 55%, at least 60%, at least65%, at least 70%, at least 75%, at least 80%, at least 85%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%identical to SEQ ID NO: 113.

In one aspect, the present disclosure provides a recombinant nucleicacid encoding a FRG-like protein, where the FRG-like protein contains aDNA-binding domain and a FRG polypeptide or a fragment thereof. In someembodiments, the FRG polypeptide or fragment thereof has an amino acidsequence that is at least 50%, at least 55%, at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% identicalto SEQ ID NO: 125.

Target Nucleic Acids of the Present Disclosure

Other aspects of the present disclosure relate to utilizing recombinantproteins to reduce the expression of one or more genes of interest inplants by binding to one or more target nucleic acids associated withthe genes of interest. The recombinant proteins may be SHH1-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins. In some embodiments, the SHH1-like proteins, SUVH2-likeproteins, SUVH9-like proteins, DMS3-like proteins, MORC6-like proteins,SUVR2-like proteins, DRD1-like proteins, RDM1-like proteins, DRM3-likeproteins, DRM2-like proteins, and/or FRG-like proteins reduce expressionof a gene of interest by binding to a target nucleic acid. In someembodiments, the SHH1-like proteins, SUVH2-like proteins, SUVH9-likeproteins, DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins,DRD1-like proteins, RDM1-like proteins, DRM3-like proteins, DRM2-likeproteins, and/or FRG-like proteins silence expression of a gene ofinterest by binding to a target nucleic acid.

In some embodiments, a target nucleic acid of the present disclosure isa nucleic acid that is located at any location within a target gene thatprovides a suitable location for reducing expression of the target gene.The target nucleic acid may be located within the coding region of atarget gene or upstream or downstream thereof. Moreover, the targetnucleic acid may reside endogenously in a target gene or may be insertedinto the gene, e.g., heterologous, for example, using techniques such ashomologous recombination. For example, a target gene of the presentdisclosure can be operably linked to a control region, such as apromoter, that contains a sequence that is recognized and bound bySHH1-like proteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-likeproteins, MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins,RDM1-like proteins, DRM3-like proteins, DRM2-like proteins, and/orFRG-like proteins of the present disclosure.

The target nucleic acid may be any given nucleic acid of interest thatcan be bound by an SHH1-like protein, a SUVH2-like protein, a SUVH9-likeprotein, a DMS3-like protein, a MORC6-like protein, a SUVR2-likeprotein, a DRD1-like protein, an RDM1-like protein, a DRM3-like protein,a DRM2-like protein, and/or an FRG-like protein of the presentdisclosure. In some embodiments, the target nucleic acid is endogenousto the plant where the expression of one or more genes is reduced by anSHH1-like protein, a SUVH2-like protein, a SUVH9-like protein, aDMS3-like protein, a MORC6-like protein, a SUVR2-like protein, aDRD1-like protein, an RDM1-like protein, a DRM3-like protein, aDRM2-like protein, and/or an FRG-like protein of the present disclosure.In some embodiments, the target nucleic acid is a transgene of interestthat has been inserted into a plant. Methods of introducing transgenesinto plants are well known in the art. Transgenes may be inserted intoplants in order to provide a production system for a desired protein, ormay be added to the genetic compliment in order to modulate themetabolism of a plant.

Examples of suitable endogenous plant genes whose expression can bereduced by an SHH1-like protein, a SUVH2-like protein, a SUVH9-likeprotein, a DMS3-like protein, a MORC6-like protein, a SUVR2-likeprotein, a DRD1-like protein, an RDM1-like protein, a DRM3-like protein,a DRM2-like protein, and/or an FRG-like protein of the presentdisclosure may include, for example, genes that prevent the enhancementof one or more desired traits and genes that prevent increased cropyields. For example, an SHH1-like protein, a SUVH2-like protein, aSUVH9-like protein, a DMS3-like protein, a MORC6-like protein, aSUVR2-like protein, a DRD1-like protein, an RDM1-like protein, aDRM3-like protein, a DRM2-like protein, and/or an FRG-like protein ofthe present disclosure may be used to reduce the expression of the geneGAI in plants, which would create plants that are less sensitive togibberellin. In embodiments relating to research, an SHH1-like protein,a SUVH2-like protein, a SUVH9-like protein, a DMS3-like protein, aMORC6-like protein, a SUVR2-like protein, a DRD1-like protein, anRDM1-like protein, a DRM3-like protein, a DRM2-like protein, and/or anFRG-like protein of the present disclosure may be utilized to silencethe expression of an endogenous gene of interest in order to generatemutant plants in which to study the function of the gene of interest.

Examples of suitable transgenes present in plants whose expression canbe reduced by an SHH1-like protein, a SUVH2-like protein, a SUVH9-likeprotein, a DMS3-like protein, a MORC6-like protein, a SUVR2-likeprotein, a DRD1-like protein, an RDM1-like protein, a DRM3-like protein,a DRM2-like protein, and/or an FRG-like protein of the presentdisclosure may include, for example, transgenes that are not useful incertain genetic backgrounds, transgenes that are harmful in certaingenetic backgrounds, and transgenes that are expressed in certaintissues that are undesirable. For example, in the case of transgenesthat are expressed in certain tissues that are undesirable, an SHH1-likeprotein, a SUVH2-like protein, a SUVH9-like protein, a DMS3-likeprotein, a MORC6-like protein, a SUVR2-like protein, a DRD1-likeprotein, an RDM1-like protein, a DRM3-like protein, a DRM2-like protein,and/or an FRG-like protein of the present disclosure can be utilized tosilence the expression of such transgenes in specific tissues atspecific times by operably linking tissue specific promoters to therecombinant polypeptides of the present disclosure. In embodimentsrelating to research, an SHH1-like protein, a SUVH2-like protein, aSUVH9-like protein, a DMS3-like protein, a MORC6-like protein, aSUVR2-like protein, a DRD1-like protein, an RDM1-like protein, aDRM3-like protein, a DRM2-like protein, and/or an FRG-like protein ofthe present disclosure may be utilized to dynamically study transgenesof interest by controlling the induction/silencing of the transgenes.

Plants of the Present Disclosure

Certain aspects of the present disclosure relate to plants containingone or more SHH1-like proteins, SUVH2-like proteins, SUVH9-likeproteins, DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins,DRD1-like proteins, RDM1-like proteins, DRM3-like proteins, DRM2-likeproteins, and/or FRG-like proteins. In certain embodiments, theSHH1-like proteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-likeproteins, MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins,RDM1-like proteins, DRM3-like proteins, DRM2-like proteins, and/orFRG-like proteins bind to one or more target nucleic acids in the plantand reduce the expression of the one or more target nucleic acids.

As used herein, a “plant” refers to any of various photosynthetic,eukaryotic multi-cellular organisms of the kingdom Plantae,characteristically producing embryos, containing chloroplasts, havingcellulose cell walls and lacking locomotion. As used herein, a “plant”includes any plant or part of a plant at any stage of development,including seeds, suspension cultures, plant cells, embryos, meristematicregions, callus tissue, leaves, roots, shoots, gametophytes,sporophytes, pollen, microspores, and progeny thereof. Also included arecuttings, and cell or tissue cultures. As used in conjunction with thepresent disclosure, plant tissue includes, without limitation, wholeplants, plant cells, plant organs, e.g., leafs, stems, roots, meristems,plant seeds, protoplasts, callus, cell cultures, and any groups of plantcells organized into structural and/or functional units.

Any plant cell may be used in the present disclosure so long as itremains viable after being transformed with a sequence of nucleic acids.Preferably, the plant cell is not adversely affected by the transductionof the necessary nucleic acid sequences, the subsequent expression ofthe proteins or the resulting intermediates.

As disclosed herein, a broad range of plant types may be modified toincorporate an SHH1-like protein, a SUVH2-like protein, a SUVH9-likeprotein, a DMS3-like protein, a MORC6-like protein, a SUVR2-likeprotein, a DRD1-like protein, an RDM1-like protein, a DRM3-like protein,a DRM2-like protein, and/or an FRG-like protein. Suitable plants thatmay be modified include both monocotyledonous (monocot) plants anddicotyledonous (dicot) plants.

Examples of suitable plants may include, for example, species of theFamily Gramineae, including Sorghum bicolor and Zea mays; species of thegenera: Cucurbita, Rosa, Vitis, Juglans, Fragaria, Lotus, Medicago,Onobrychis, Trifolium, Trigonella, Vigna, Citrus, Linum, Geranium,Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa,Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia,Digitalis, Majorana, Ciahorium, Helianthus, Lactuca, Bromus, Asparagus,Antirrhinum, Heterocallis, Nemesis, Pelargonium, Panieum, Pennisetum,Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Pisum,Phaseolus, Lolium, Oryza, Avena, Hordeum, Secale, and Triticum.

In some embodiments, plant cells may include, for example, those fromcorn (Zea mays), canola (Brassica napus, Brassica rapa ssp.), Brassicaspecies useful as sources of seed oil, alfalfa (Medicago sativa), rice(Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghumvulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet(Panicum miliaceum), foxtail millet (Setaria italica), finger millet(Eleusine coracana)), sunflower (Helianthus annuus), safflower(Carthamus tinctorius), wheat (Triticum aestivum), duckweed (Lemna),soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanumtuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense,Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihotesculenta), coffee (Coffea spp.), coconut (Cocos nucijra), pineapple(Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao),tea (Camellia sinensis), banana (Musa spp.), avocado (Persea americana),fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica),olive (Olea europaea), papaya (Carica papaya), cashew (Anacardiumoccidentale), macadamia (Macadamia spp.), almond (Prunus amygdalus),sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, barley,vegetables, ornamentals, and conifers.

Examples of suitable vegetables plants may include, for example,tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa),green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas(Lathyrus spp.), and members of the genus Cucumis such as cucumber (C.sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo).

Examples of suitable ornamental plants may include, for example, azalea(Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus(Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.),daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation(Dianthus caryophyllus), poinsettia (Euphorbiapulcherrima), andchrysanthemum.

Examples of suitable conifer plants may include, for example, loblollypine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinusponderosa), lodgepole pine (Pinus contorta), Monterey pine (Pinusradiata), Douglas-fir (Pseudotsuga menziesii), Western hemlock (Isugacanadensis), Sitka spruce (Picea glauca), redwood (Sequoiasempervirens), silver fir (Abies amabilis), balsam fir (Abies balsamea),Western red cedar (Thuja plicata), and Alaska yellow-cedar(Chamaecyparis nootkatensis).

Examples of suitable leguminous plants may include, for example, guar,locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, limabean, fava bean, lentils, chickpea, peanuts (Arachis sp.), crown vetch(Vicia sp.), hairy vetch, adzuki bean, lupine (Lupinus sp.), trifolium,common bean (Phaseolus sp.), field bean (Pisum sp.), clover (Melilotussp.) Lotus, trefoil, lens, and false indigo.

Examples of suitable forage and turf grass may include, for example,alfalfa (Medicago s sp.), orchard grass, tall fescue, perennialryegrass, creeping bent grass, and redtop.

Examples of suitable crop plants and model plants may include, forexample, Arabidopsis, corn, rice, alfalfa, sunflower, canola, soybean,cotton, peanut, sorghum, wheat, tobacco, and lemna.

The plants of the present disclosure may be genetically modified in thatrecombinant nucleic acids have been introduced into the plants, and assuch the genetically modified plants do not occur in nature. A suitableplant of the present disclosure is one capable of expressing one or morenucleic acid constructs encoding one or more recombinant proteins. Therecombinant proteins encoded by the nucleic acids may be SHH1-likeproteins, SUVH2-like proteins, SUVH9-like proteins, DMS3-like proteins,MORC6-like proteins, SUVR2-like proteins, DRD1-like proteins, RDM1-likeproteins, DRM3-like proteins, DRM2-like proteins, and/or FRG-likeproteins.

As used herein, the terms “transgenic plant” and “genetically modifiedplant” are used interchangeably and refer to a plant which containswithin its genome a recombinant nucleic acid. Generally, the recombinantnucleic acid is stably integrated within the genome such that thepolynucleotide is passed on to successive generations. However, incertain embodiments, the recombinant nucleic acid is transientlyexpressed in the plant. The recombinant nucleic acid may be integratedinto the genome alone or as part of a recombinant expression cassette.“Transgenic” is used herein to include any cell, cell line, callus,tissue, plant part or plant, the genotype of which has been altered bythe presence of exogenous nucleic acid including those transgenicsinitially so altered as well as those created by sexual crosses orasexual propagation from the initial transgenic.

“Recombinant nucleic acid” or “heterologous nucleic acid” or“recombinant polynucleotide” as used herein refers to a polymer ofnucleic acids wherein at least one of the following is true: (a) thesequence of nucleic acids is foreign to (i.e., not naturally found in) agiven host cell; (b) the sequence may be naturally found in a given hostcell, but in an unnatural (e.g., greater than expected) amount; or (c)the sequence of nucleic acids contains two or more subsequences that arenot found in the same relationship to each other in nature. For example,regarding instance (c), a recombinant nucleic acid sequence will havetwo or more sequences from unrelated genes arranged to make a newfunctional nucleic acid. Specifically, the present disclosure describesthe introduction of an expression vector into a plant cell, where theexpression vector contains a nucleic acid sequence coding for a proteinthat is not normally found in a plant cell or contains a nucleic acidcoding for a protein that is normally found in a plant cell but is underthe control of different regulatory sequences. With reference to theplant cell's genome, then, the nucleic acid sequence that codes for theprotein is recombinant. A protein that is referred to as recombinantgenerally implies that it is encoded by a recombinant nucleic acidsequence in the plant cell.

A “recombinant” polypeptide, protein, or enzyme of the presentdisclosure, is a polypeptide, protein, or enzyme that is encoded by a“recombinant nucleic acid” or “heterologous nucleic acid” or“recombinant polynucleotide.”

In some embodiments, the genes encoding the recombinant proteins in theplant cell may be heterologous to the plant cell. In certainembodiments, the plant cell does not naturally produce the recombinantproteins, and contains heterologous nucleic acid constructs capable ofexpressing one or more genes necessary for producing those molecules.

Expression of Recombinant Proteins in Plants

An SHH1-like protein, a SUVH2-like protein, a SUVH9-like protein, aDMS3-like protein, a MORC6-like protein, a SUVR2-like protein, aDRD1-like protein, an RDM1-like protein, a DRM3-like protein, aDRM2-like protein, and/or an FRG-like protein of the present disclosuremay be introduced into plant cells via any suitable methods known in theart. For example, an SHH1-like protein, a SUVH2-like protein, aSUVH9-like protein, a DMS3-like protein, a MORC6-like protein, aSUVR2-like protein, a DRD1-like protein, an RDM1-like protein, aDRM3-like protein, a DRM2-like protein, and/or an FRG-like protein canbe exogenously added to plant cells and the plant cells are maintainedunder conditions such that the SHH1-like protein, a SUVH2-like protein,a SUVH9-like protein, a DMS3-like protein, a MORC6-like protein, aSUVR2-like protein, a DRD1-like protein, an RDM1-like protein, aDRM3-like protein, a DRM2-like protein, and/or an FRG-like protein bindsto one or more target nucleic acids and reduces the expression of thetarget nucleic acids in the plant cells. Alternatively, a recombinantnucleic acid encoding an SHH1-like protein, a SUVH2-like protein, aSUVH9-like protein, a DMS3-like protein, a MORC6-like protein, aSUVR2-like protein, a DRD1-like protein, an RDM1-like protein, aDRM3-like protein, a DRM2-like protein, and/or an FRG-like protein ofthe present disclosure can be expressed in plant cells and the plantcells are maintained under conditions such that the expressed SHH1-likeprotein, a SUVH2-like protein, a SUVH9-like protein, a DMS3-likeprotein, a MORC6-like protein, a SUVR2-like protein, a DRD1-likeprotein, an RDM1-like protein, a DRM3-like protein, a DRM2-like protein,and/or an FRG-like protein binds to one or more target nucleic acids andreduces the expression of the target gene in the plant cells.Additionally, in some embodiments, an SHH1-like protein, a SUVH2-likeprotein, a SUVH9-like protein, a DMS3-like protein, a MORC6-likeprotein, a SUVR2-like protein, a DRD1-like protein, an RDM1-likeprotein, a DRM3-like protein, a DRM2-like protein, and/or an FRG-likeprotein of the present disclosure may be transiently expressed in aplant via viral infection of the plant, or by introducing an SHH1-likeprotein-encoding RNA, a SUVH2-like protein-encoding RNA, a SUVH9-likeprotein-encoding RNA, a DMS3-like protein-encoding RNA, a MORC6-likeprotein-encoding RNA, a SUVR2-like protein-encoding RNA, a DRD1-likeprotein-encoding RNA, an RDM1-like protein-encoding RNA, a DRM3-likeprotein-encoding RNA, a DRM2-like protein-encoding RNA, and/or anFRG-like protein-encoding RNA into a plant to temporarily reduce orsilence the expression of a gene of interest. Methods of introducingrecombinant proteins via viral infection or via the introduction of RNAsinto plants are well known in the art. For example, Tobacco rattle virus(TRV) has been successfully used to introduce zinc finger nucleases inplants to cause genome modification (“Nontransgenic Genome Modificationin Plant Cells”, Plant Physiology 154:1079-1087 (2010)).

A recombinant nucleic acid encoding an SHH1-like protein, a SUVH2-likeprotein, a SUVH9-like protein, a DMS3-like protein, a MORC6-likeprotein, a SUVR2-like protein, a DRD1-like protein, an RDM1-likeprotein, a DRM3-like protein, a DRM2-like protein, and/or an FRG-likeprotein of the present disclosure can be expressed in a plant with anysuitable plant expression vector. Typical vectors useful for expressionof recombinant nucleic acids in higher plants are well known in the artand include, without limitation, vectors derived from the tumor-inducing(Ti) plasmid of Agrobacterium tumefaciens (e.g., see Rogers et al.,Meth. in Enzymol. (1987) 153:253-277). These vectors are plantintegrating vectors in that on transformation, the vectors integrate aportion of vector DNA into the genome of the host plant. Exemplary A.tumefaciens vectors useful herein are plasmids pKYLX6 and pKYLX7 (e.g.,see of Schardl et al., Gene (1987) 61:1-11; and Berger et al., Proc.Natl. Acad. Sci. USA (1989) 86:8402-8406); and plasmid pBI 101.2 that isavailable from Clontech Laboratories, Inc. (Palo Alto, Calif.).

In addition to regulatory domains, an SHH1-like protein, a SUVH2-likeprotein, a SUVH9-like protein, a DMS3-like protein, a MORC6-likeprotein, a SUVR2-like protein, a DRD1-like protein, an RDM1-likeprotein, a DRM3-like protein, a DRM2-like protein, and/or an FRG-likeprotein of the present disclosure can be expressed as a fusion proteinthat is coupled to, for example, a maltose binding protein (“MBP”),glutathione S transferase (GST), hexahistidine, c-myc, or the FLAGepitope for ease of purification, monitoring expression, or monitoringcellular and subcellular localization.

Moreover, a recombinant nucleic acid encoding an SHH1-like protein, aSUVH2-like protein, a SUVH9-like protein, a DMS3-like protein, aMORC6-like protein, a SUVR2-like protein, a DRD1-like protein, anRDM1-like protein, a DRM3-like protein, a DRM2-like protein, and/or anFRG-like protein of the present disclosure can be modified to improveexpression of the recombinant protein in plants by using codonpreference. When the recombinant nucleic acid is prepared or alteredsynthetically, advantage can be taken of known codon preferences of theintended plant host where the nucleic acid is to be expressed. Forexample, recombinant nucleic acids of the present disclosure can bemodified to account for the specific codon preferences and GC contentpreferences of monocotyledons and dicotyledons, as these preferenceshave been shown to differ (Murray et al., Nucl. Acids Res. (1989) 17:477-498).

In some embodiments, SHH1-like proteins, SUVH2-like proteins, SUVH9-likeproteins, DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins,DRD1-like proteins, RDM1-like proteins, DRM3-like proteins, DRM2-likeproteins, and/or FRG-like proteins of the present disclosure can be usedto create functional “gene knockout” mutations in a plant by repressionof the target gene expression. Repression may be of a structural gene,e.g., one encoding a protein having for example enzymatic activity, orof a regulatory gene, e.g., one encoding a protein that in turnregulates expression of a structural gene.

The present disclosure further provides expression vectors containing anSHH1-like protein-encoding nucleic acid, a SUVH2-like protein-encodingnucleic acid, a SUVH9-like protein-encoding nucleic acid, a DMS3-likeprotein-encoding nucleic acid, a MORC6-like protein-encoding nucleicacid, a SUVR2-like protein-encoding nucleic acid, a DRD1-likeprotein-encoding nucleic acid, an RDM1-like protein-encoding nucleicacid, a DRM3-like protein-encoding nucleic acid, a DRM2-likeprotein-encoding nucleic acid, and/or an FRG-like protein-encodingnucleic acid of the present disclosure. A nucleic acid sequence codingfor the desired recombinant nucleic acid of the present disclosure canbe used to construct a recombinant expression vector which can beintroduced into the desired host cell. A recombinant expression vectorwill typically contain a nucleic acid encoding a recombinant protein ofthe present disclosure, operably linked to transcriptional initiationregulatory sequences which will direct the transcription of the nucleicacid in the intended host cell, such as tissues of a transformed plant.

For example, plant expression vectors may include (1) a cloned plantgene under the transcriptional control of 5′ and 3′ regulatory sequencesand (2) a dominant selectable marker. Such plant expression vectors mayalso contain, if desired, a promoter regulatory region (e.g., oneconferring inducible or constitutive, environmentally- ordevelopmentally-regulated, or cell- or tissue-specific/selectiveexpression), a transcription initiation start site, a ribosome bindingsite, an RNA processing signal, a transcription termination site, and/ora polyadenylation signal.

A plant promoter, or functional fragment thereof, can be employed tocontrol the expression of a recombinant nucleic acid of the presentdisclosure in regenerated plants. The selection of the promoter used inexpression vectors will determine the spatial and temporal expressionpattern of the recombinant nucleic acid in the modified plant, e.g., theSHH1-like protein-encoding nucleic acid, a SUVH2-like protein-encodingnucleic acid, a SUVH9-like protein-encoding nucleic acid, a DMS3-likeprotein-encoding nucleic acid, a MORC6-like protein-encoding nucleicacid, a SUVR2-like protein-encoding nucleic acid, a DRD1-likeprotein-encoding nucleic acid, an RDM1-like protein-encoding nucleicacid, a DRM3-like protein-encoding nucleic acid, a DRM2-likeprotein-encoding nucleic acid, and/or an FRG-like protein-encodingnucleic acid is only expressed in the desired tissue or at a certaintime in plant development or growth. Certain promoters will expressrecombinant nucleic acids in all plant tissues and are active under mostenvironmental conditions and states of development or celldifferentiation (i.e., constitutive promoters). Other promoters willexpress recombinant nucleic acids in specific cell types (such as leafepidermal cells, mesophyll cells, root cortex cells) or in specifictissues or organs (roots, leaves or flowers, for example) and theselection will reflect the desired location of accumulation of the geneproduct. Alternatively, the selected promoter may drive expression ofthe recombinant nucleic acid under various inducing conditions.

Examples of suitable constitutive promoters may include, for example,the core promoter of the Rsyn7, the core CaMV 35S promoter (Odell etal., Nature (1985) 313:810-812), CaMV 19S (Lawton et al., 1987), riceactin (Wang et al., 1992; U.S. Pat. No. 5,641,876; and McElroy et al.,Plant Cell (1985) 2:163-171); ubiquitin (Christensen et al., Plant Mol.Biol. (1989)12:619-632; and Christensen et al., Plant Mol. Biol. (1992)18:675-689), pEMU (Last et al., Theor. Appl. Genet. (1991) 81:581-588),MAS (Velten et al., EMBO J. (1984) 3:2723-2730), nos (Ebert et al.,1987), Adh (Walker et al., 1987), the P- or 2′-promoter derived fromT-DNA of Agrobacterium tumefaciens, the Smas promoter, the cinnamylalcohol dehydrogenase promoter (U.S. Pat. No. 5,683,439), the Nospromoter, the pEmu promoter, the rubisco promoter, the GRP 1-8 promoter,and other transcription initiation regions from various plant genesknown to those of skilled artisans, and constitutive promoters describedin, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121;5,569,597; 5,466,785; 5,399,680; 5,268,463; and 5, 608,142.

Examples of suitable tissue specific promoters may include, for example,the lectin promoter (Vodkin et al., 1983; Lindstrom et al., 1990), thecorn alcohol dehydrogenase 1 promoter (Vogel et al., 1989; Dennis etal., 1984), the corn light harvesting complex promoter (Simpson, 1986;Bansal et al., 1992), the corn heat shock protein promoter (Odell etal., Nature (1985) 313:810-812; Rochester et al., 1986), the pea smallsubunit RuBP carboxylase promoter (Poulsen et al., 1986; Cashmore etal., 1983), the Ti plasmid mannopine synthase promoter (Langridge etal., 1989), the Ti plasmid nopaline synthase promoter (Langridge et al.,1989), the petunia chalcone isomerase promoter (Van Tunen et al., 1988),the bean glycine rich protein 1 promoter (Keller et al., 1989), thetruncated CaMV 35s promoter (Odell et al., Nature (1985) 313:810-812),the potato patatin promoter (Wenzler et al., 1989), the root cellpromoter (Conkling et al., 1990), the maize zein promoter (Reina et al.,1990; Kriz et al., 1987; Wandelt and Feix, 1989; Langridge and Feix,1983; Reina et al., 1990), the globulin-1 promoter (Belanger and Kriz etal., 1991), the α-tubulin promoter, the cab promoter (Sullivan et al.,1989), the PEPCase promoter (Hudspeth & Grula, 1989), the R genecomplex-associated promoters (Chandler et al., 1989), and the chalconesynthase promoters (Franken et al., 1991).

Alternatively, the plant promoter can direct expression of a recombinantnucleic acid of the present disclosure in a specific tissue or may beotherwise under more precise environmental or developmental control.Such promoters are referred to here as “inducible” promoters.Environmental conditions that may affect transcription by induciblepromoters include, without limitation, pathogen attack, anaerobicconditions, or the presence of light. Examples of inducible promotersinclude, without limitation, the AdhI promoter which is inducible byhypoxia or cold stress, the Hsp70 promoter which is inducible by heatstress, and the PPDK promoter which is inducible by light. Examples ofpromoters under developmental control include, without limitation,promoters that initiate transcription only, or preferentially, incertain tissues, such as leaves, roots, fruit, seeds, or flowers. Anexemplary promoter is the anther specific promoter 5126 (U.S. Pat. Nos.5,689,049 and 5,689,051). The operation of a promoter may also varydepending on its location in the genome. Thus, an inducible promoter maybecome fully or partially constitutive in certain locations.

Moreover, any combination of a constitutive or inducible promoter, and anon-tissue specific or tissue specific promoter may be used to controlthe expression of an SHH1-like protein, a SUVH2-like protein, aSUVH9-like protein, a DMS3-like protein, a MORC6-like protein, aSUVR2-like protein, a DRD1-like protein, an RDM1-like protein, aDRM3-like protein, a DRM2-like protein, and/or an FRG-like protein.

Both heterologous and endogenous promoters can be employed to directexpression of recombinant nucleic acids of the present disclosure.Accordingly, in certain embodiments, expression of an SHH1-likeprotein-encoding nucleic acid, a SUVH2-like protein-encoding nucleicacid, a SUVH9-like protein-encoding nucleic acid, a DMS3-likeprotein-encoding nucleic acid, a MORC6-like protein-encoding nucleicacid, a SUVR2-like protein-encoding nucleic acid, a DRD1-likeprotein-encoding nucleic acid, an RDM1-like protein-encoding nucleicacid, a DRM3-like protein-encoding nucleic acid, a DRM2-likeprotein-encoding nucleic acid, and/or an FRG-like protein-encodingnucleic acid of the present disclosure is under the control of itsrespective endogenous promoter. In other embodiments, expression of anSHH1-like protein-encoding nucleic acid, a SUVH2-like protein-encodingnucleic acid, a SUVH9-like protein-encoding nucleic acid, a DMS3-likeprotein-encoding nucleic acid, a MORC6-like protein-encoding nucleicacid, a SUVR2-like protein-encoding nucleic acid, a DRD1-likeprotein-encoding nucleic acid, an RDM1-like protein-encoding nucleicacid, a DRM3-like protein-encoding nucleic acid, a DRM2-likeprotein-encoding nucleic acid, and/or an FRG-like protein-encodingnucleic acid of the present disclosure is under the control of aheterologous promoter. Additionally, an endogenous SHH1 gene, SUVH2gene, SUVH9 gene, DMS3 gene, MORC6 gene, SUVR2 gene, DRD1 gene, RDM1gene, DRM3 gene, DRM2 gene, and/or FRG gene of the present disclosurecan be modified using a knock-in approach, so that the modified genewill be under the control of its respective endogenous elements.Alternatively, a modified form of an entire SHH1, SUVH2, SUVH9, DMS3,MORC6, SUVR2, DRD1, RDM1, DRM3, DRM2, and/or FRG genomic sequence may beintroduced into a plant, so that the modified/recombinant gene will beunder the control of its endogenous elements and the wild-type generemains intact. Any or all of these techniques may also be combined todirect the expression of a recombinant nucleic acid of the presentdisclosure.

The recombinant nucleic acids of the present disclosure, such as anSHH1-like protein-encoding nucleic acid, a SUVH2-like protein-encodingnucleic acid, a SUVH9-like protein-encoding nucleic acid, a DMS3-likeprotein-encoding nucleic acid, a MORC6-like protein-encoding nucleicacid, a SUVR2-like protein-encoding nucleic acid, a DRD1-likeprotein-encoding nucleic acid, an RDM1-like protein-encoding nucleicacid, a DRM3-like protein-encoding nucleic acid, a DRM2-likeprotein-encoding nucleic acid, and/or an FRG-like protein-encodingnucleic acid, and/or a vector housing a recombinant nucleic acid of thepresent disclosure, may also contain a regulatory sequence that servesas a 3′ terminator sequence. One of skill in the art would readilyrecognize a variety of terminators that may be used in the recombinantnucleic acids of the present disclosure. For example, a recombinantnucleic acid of the present disclosure may contain a 3′ NOS terminator.Further, a native terminator from an SHH1-like protein-encoding nucleicacid, a SUVH2-like protein-encoding nucleic acid, a SUVH9-likeprotein-encoding nucleic acid, a DMS3-like protein-encoding nucleicacid, a MORC6-like protein-encoding nucleic acid, a SUVR2-likeprotein-encoding nucleic acid, a DRD1-like protein-encoding nucleicacid, an RDM1-like protein-encoding nucleic acid, a DRM3-likeprotein-encoding nucleic acid, a DRM2-like protein-encoding nucleicacid, and/or an FRG-like protein-encoding nucleic acid may also be usedin the recombinant nucleic acids of the present disclosure.

Plant transformation protocols as well as protocols for introducingrecombinant nucleic acids of the present disclosure into plants may varydepending on the type of plant or plant cell, e.g., monocot or dicot,targeted for transformation. Suitable methods of introducing recombinantnucleic acids of the present disclosure into plant cells and subsequentinsertion into the plant genome include, without limitation,microinjection (Crossway et al., Biotechniques (1986) 4:320-334),electroporation (Riggs et al., Proc. Natl. Acad Sci. USA (1986)83:5602-5606), Agrobacterium-mediated transformation (U.S. Pat. No.5,563,055), direct gene transfer (Paszkowski et al., EMBO J. (1984)3:2717-2722), and ballistic particle acceleration (U.S. Pat. No.4,945,050; Tomes et al. (1995). “Direct DNA Transfer into Intact PlantCells via Microprojectile Bombardment,” in Plant Cell, Tissue, and OrganCulture: Fundamental Methods, ed. Gamborg and Phillips (Springer-Verlag,Berlin); and McCabe et al., Biotechnology (1988) 6:923-926).

Additionally, SHH1-like proteins, SUVH2-like proteins, SUVH9-likeproteins, DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins,DRD1-like proteins, RDM1-like proteins, DRM3-like proteins, DRM2-likeproteins, and/or FRG-like proteins of the present disclosure can betargeted to a specific organelle within a plant cell. Targeting can beachieved by providing the recombinant protein with an appropriatetargeting peptide sequence. Examples of such targeting peptides include,without limitation, secretory signal peptides (for secretion or cellwall or membrane targeting), plastid transit peptides, chloroplasttransit peptides, mitochondrial target peptides, vacuole targetingpeptides, nuclear targeting peptides, and the like (e.g., see Reiss etal., Mol. Gen. Genet. (1987) 209(1):116-121; Settles and Martienssen,Trends Cell Biol (1998) 12:494-501; Scott et al., J Biol Chem (2000)10:1074; and Luque and Correas, J Cell Sci (2000) 113:2485-2495).

The modified plant may be grown into plants in accordance withconventional ways (e.g., see McCormick et al., Plant Cell. Reports(1986) 81-84.). These plants may then be grown, and pollinated witheither the same transformed strain or different strains, with theresulting hybrid having the desired phenotypic characteristic. Two ormore generations may be grown to ensure that the subject phenotypiccharacteristic is stably maintained and inherited and then seedsharvested to ensure the desired phenotype or other property has beenachieved.

Methods of Reducing Gene Expression in Plants

Further aspects of the present disclosure relate to methods for reducingexpression of one or more target nucleic acids, such as genes, in aplant by utilizing SHH1-like proteins, SUVH2-like proteins, SUVH9-likeproteins, DMS3-like proteins, MORC6-like proteins, SUVR2-like proteins,DRD1-like proteins, RDM1-like proteins, DRM3-like proteins, DRM2-likeproteins, and/or FRG-like proteins. In one aspect, the presentdisclosure provides a method for reducing expression of one or moretarget nucleic acids in a plant, by providing a plant containing one ormore recombinant polypeptides of the present disclosure, and growing theplant under conditions whereby the recombinant polypeptide(s) binds toone or more target nucleic acids of the present disclosure, therebyreducing expression of the one or more target genes. Any plant describedherein and containing a recombinant polypeptide of the presentdisclosure may be used.

Growing conditions sufficient for the recombinant polypeptide expressedin the plant to bind to and reduce the expression of one or more targetnucleic acids of the present disclosure are well known in the art andinclude any suitable growing conditions disclosed herein. Typically, theplant is grown under conditions sufficient to express the recombinantpolypeptide, such as an SHH1-like protein, a SUVH2-like protein, aSUVH9-like protein, a DMS3-like protein, a MORC6-like protein, aSUVR2-like protein, a DRD1-like protein, an RDM1-like protein, aDRM3-like protein, a DRM2-like protein, and/or an FRG-like protein ofthe present disclosure, and for the expressed recombinant polypeptide tobe localized to the nucleus of cells of the plant in order to bind toand reduce the expression of the target nucleic acids. Generally, theconditions sufficient for the expression of the recombinant polypeptidewill depend on the promoter used to control the expression of therecombinant polypeptide. For example, if an inducible promoter isutilized, expression of the recombinant polypeptide in a plant willrequire that the plant to be grown in the presence of the inducer.

It is to be understood that while the present disclosure has beendescribed in conjunction with the preferred specific embodimentsthereof, the foregoing description is intended to illustrate and notlimit the scope of the present disclosure. Other aspects, advantages,and modifications within the scope of the present disclosure will beapparent to those skilled in the art to which the present disclosurepertains.

The following examples are offered to illustrate provided embodimentsand are not intended to limit the scope of the present disclosure.

EXAMPLES Example 1

The following Example relates to the characterization of the Arabidopsisthaliana protein SHH1 and its involvement in promoting RNA-directed DNAmethylation and gene silencing.

Materials and Methods

ChIP-Seq, BS-Seq and siRNA-Seq Library Construction and Sequencing

The first replicate of ChIP-seq libraries (NRPD1-Flag and Col) wasgenerated using the Ovation Ultralow IL Multiplex System (NuGEN) whilethe second replicate (NRPD1-Flag, NRPD1-Flag; shh1, and Col) wasgenerated using the Ovation Ultralow DR Multiplex System (NuGEN). Bothsets of ChIP-seq libraries used 18 cycles for the library amplificationstep. BS-seq libraries were generated as previously reported (Cokus etal., 2008). siRNA-seq libraries were generated using the small RNATruSeq kit (Illumina) following the manufacturer instructions with theexception that 15 cycles were used during the amplification step. Thewild-type (Col) and impel BS-seq libraries used in this study werepreviously published (Zhong et al., 2012) and were subsequentlyreanalyzed. All libraries were sequenced using the HiSeq 2000 platformfollowing manufacturer instructions (Illumina) at a length of 50 bp.

Mapping and Processing of Reads

Sequenced reads were base-called using the standard Illumina pipeline.For ChIP-seq and BS-seq libraries, only full 50 nt reads were retained,whereas for siRNA-seq libraries, reads had adapter sequence trimmed andwere retained if they were between 18 nt and 28 nt in length. ForChIP-seq and siRNA-seq libraries, reads were mapped to the Arabidopsisgenome (TAIR8) with Bowtie (Langmead et al., 2009) and only perfectmatches that mapped uniquely to the genome were retained for furtheranalysis although the total number of mapping reads, unique andnon-unique, were used when normalizing the siRNA-seq libraries to totalnumber of reads per library. For BS-seq libraries, reads were mappedusing the BSseeker wrapper for Bowtie (Chen et al., 2010). For ChIP-seqand BS-seq, identical reads were collapsed into one read, whereas forsiRNA-seq identical reads were retained. For methylation analysis,percent methylation was calculated as previously reported (Cokus et al.,2008) with the unmethylated chloroplast genome serving as the measure ofnon-bisulfite converted background methylation. For the second replicateof ChIP-seq, the NRPD1-Flag and Col libraries were sampled down to matchthe read total of the smaller library (the NRPD1-Flag; shh1 library).

DNA Methylation Analysis

For assessment of DNA methylation at siRNA clusters, only those clusterswith at least one cytosine in the respective class being assayed (CG,CHG, or CHH), were considered. For calculating significance levels ofmethylation change via the Mann-Whitney U test of methylation levels forclusters within the different subclasses (FIG. 1E) the number ofclusters within each subclass was down sampled to the smallest subclass(the drm2/nrpe1 subclass) to allow for comparable significance valuesbetween subclasses.

Identification of siRNA Clusters

Small RNA clusters in the Arabidopsis genome were defined in a mannersimilar to a previously published approach (Heisel et al., 2008). Inbrief, the genome was divided into 200 bp bins, and the average coverageper bin of non-identical siRNA reads was calculated in two technicalreplicates of the wild-type (Col) library. This average was used assaythe significance of the number of non-identical reads at a given bin inwild-type plants, assuming a Poisson distribution of such counts. In theR environment a Poisson exact test was carried out for each bin, andbins with a P-value less than 1e-5 in each wild-type technical replicatewere considered as clusters.

Once clusters were defined, comparisons between read counts, includingidentical reads, were carried out for each mutant and the wild-type(Col) library using a Fisher's Exact Test. Resultant P-values wereBenjamini-Hochberg adjusted to estimate FDRs, and clusters reduced in amutant background at a FDR<1e-10 were then considered to be dependent onthe wild-type function the mutant protein. For boxplot analysis of siRNAlevels, the first technical replicate of the Col library was used asrepresentative of Col siRNA levels. For calculating significance levelsof siRNA change via the Mann-Whitney U test of siRNA levels for clusterswithin the different genotypic subclassess (FIG. 1D) the number ofclusters within each subclass was down sampled to the smallest subclass(the drm2/nrpe1 subclass) to allow for comparable significance valuesbetween subclasses.

Identification of NRPD1 Peaks

The R package BayesPeak (Spyrou et al., 2009; Cairns et al., 2011) wasused to identify regions of Pol-IV enrichment in a NRPD1-Flag ChIP-seqlibrary as compared to a paired Col ChIP-seq control library done inparallel. Only high scoring peaks (PP>0.999) identified in bothNRPD1-Flag ChIP-seq replicates (928 peaks) were retained for furtheranalysis. For the purposes of assaying overlap of Pol IV peaks withsiRNA clusters, “overlap” was called when >=1 bp of a peak overlaps witha locus.

To classify peaks as SHH1-dependent, -independent, or -enhanced, readcounts over Pol IV peaks were compared between the NRPD1-Flag andNRPD1-Flag; shhl ChIP-seq libraries, and significance was assessed usingFisher's Exact Test. Resultant P-values were Benjamini-Hochberg adjustedto estimate FDRs. Peaks with a loss of NRPD1 signal in the shhl libraryat a FDR<0.001 were considered SHH1-dependent. Similarly, peaks thatgained signal in shhl at a FDR<0.001 were considered SHH1-enhanced.Peaks that fell into neither of these categories were consideredSHH1-independent.

Protein Preparation

The gene encoding the SAWADEE domain of at SHH1 (residues 125-258) wascloned into a self-modified vector, which fuses a hexa-histidine tagplus a yeast sumo tag onto the N terminus of the target gene. Theplasmid was transformed into the E. coli strain BL21 (DE3) RIL(Stratagene). The cells were cultured at 37° C. until the OD600 reached0.8 and then the media was cooled to 20° C. and 0.2 mM IPTG was added toinduce protein expression overnight. The recombinant expressed proteinwas first purified using a HisTrap FF column (GE Healthcare). Thehexa-histidine-sumo tag was cleavage by the Ulp 1 protease and removedby passing through a second HisTrap FF column. The pooled target proteinwas further purified using a Q FastFlow column and a Hiload SuperdexG200 16/60 column (GE Healthcare) with buffer (150 mM NaCl, 20 mM TrispH 8.0, and 5 mM DTT). In order to prepare the Se-methionine substitutedprotein, Leu200 and Leu218 of the SAWADEE domain were mutated tomethionine using a QuikChange Site Directed Mutagenesis Kit(Stratagene). The Se-methionine substituted SAWADEE protein was purifiedusing the same protocol as the wild-type protein. Peptides weresynthesized at a peptide synthesis facility.

Crystallization

Crystallization of the SAWADEE domain was conducted at 4° C. using thesitting drop vapor diffusion method by mixing 1 μl of protein sample ata concentration of 5 mg/ml and 1 μl of reservoir solution (0.2 M NH4Fand 20% PEG 3350), which was equilibrated against a 0.4 ml reservoir.4-Cyclohexyl-1-Butyl-P-D-Maltoside (CYMAL®-4, Hampton Research) wasadded in the drop with a final concentration of 7.6 mM as an additive,which resulted in considerable improvement in crystal quality. Thinplate-shaped crystals appeared within 2 days. To generate crystals ofcomplexes of SAWADEE domain with modified H3 peptides, the SAWADEEdomain was mixed with peptides at a molar ratio of 1:2 at 4° C. for 1hour. The crystals of the different complexes were grown under the sameconditions as described for free SAWADEE protein. All the crystals weresoaked into a reservoir solution supplemented with 20% glycerol for 2minutes. The crystals were then mounted on a nylon loop for diffractiondata collection. The diffraction data from the native SAWADEE proteinand its Se-methionine substituted counterpart were collected at theNE-CAT beamline 24ID-C, Advanced Photon Source (APS), Argonne NationalLaboratory, Chicago, at the zinc peak and selenium peak, respectively.The data of the complex of the H3K9me3 peptide bound to the SAWADEEdomain were collected at beamline X29A, National Synchrotron LightSource (NSLS) at Brookhaven National Laboratory, New York. The data onthe SAWADEE domain in complex with H3K9me2, H3K9me1 and H3K4me1K9me1peptides were collected at APS 241D-E. All the crystallographic datawere processed with the HKL2000 program (Otwinowski et al., 2011).

Structure Determination and Refinement

The structure of the selenomethionine-substituted SAWADEE domain wassolved using the single-wavelength anomalous dispersion (SAD) method asimplemented in the Phenix program (Adams et al., 2010). The modelbuilding was carried out using the Coot program (Emsley et al., 2010)and structural refinement using the Phenix program. The structure of thewild type SAWADEE domain in the free state was solved using themolecular replacement method using the Phenix program. Zn2+ ions wereidentified and further confirmed by anomalous signal scattering. All thestructures of SAWADEE domain in complexes with different modified H3peptides were solved using the molecular replacement method with thesame protocol as the native protein. Throughout the refinement, a free Rfactor was calculated using 5% random chosen reflections. Thestereochemistry of the structural models were analyzed using theProcheck program (Laskowski et al., 1993). All the molecular graphicswere generated with the Pymol program (DeLano Scientific LLC).

Isothermal Titration Calorimetry

All the binding experiments were performed on a Microcal calorimeter ITC200 instrument at 6° C. First, protein samples were dialyzed overnightagainst a buffer of 100 mM NaCl, 2 mM β-mercaptoethanol and 20 mM HEPES,pH 7.5, at 4° C. Then the protein samples were diluted and thelyophilized peptides were dissolved with the same buffer. The titrationwas performed according to standard protocol and the data were fit usingthe Origin 7.0 program with a 1:1 binding model.

Modified Peptide Array Binding

A GST-SHH1 SAWADEE domain (125-258aa) construct was generated in thepENTR/TEV/D plasmid (Invitrogen), recombined into the pDEST 15 plasmid(Invitrogen) and transformed into the Rosetta 2 (DE3) bacterial cellline (Novagen). Protein expression was induced by the addition of 500 μLof 1M IPTG per 500 mL at an OD of 0.6 and cultures were grown at 16° C.overnight. At the time of induction the media was supplemented with 500μL of 500 mM ZnSO4. The GST fusion protein was then purified aspreviously described (Johnson et al., 2008) and dialyzed into storagebuffer (50 mM Tris pH 6.8, 300 mM NaCl, 40% glycerol, 2 mM DTT, 0.1%triton X-100). The purified GST-SHH1 (125-258aa) protein was used toprobe a MODified™ Histone Peptide Array (Active Motif) under thefollowing conditions: The array was blocked at 25° C. for 45 mM in a 5%milk 1×TBS solution, washed three times in a 1×TBS-T solution at 25° C.for 5 minutes, and then probed overnight at 4° C. with the GST-SHH1SAWADEE domain protein at a concentration of 6.5 μg/mL in Binding Buffer(50 mM HEPES pH7.5, 50 mM NaCl, 5% glycerol, 0.4 mg/mL BSA, 2 mM DTT).The array was then washed three times as above, and probed an HRPconjugated GST antibody at a 1:5000 dilution at 25° C. for 1 hour. Thearray then washed as detailed above and developed using an ECL Plus kit(GE healthcare).

Plant Lines, Site-Directed Mutagenesis, Southern and Western Blotting

The various previously characterized Arabidopsis RdDM mutant alleles,the complementing SHH1-3×Myc-BLRP transgenic plant line, and thepSHH1::SHH1-3×Myc-BLRP construct used are as previously described (Lawet al., 2011). The pol-iv and pol-v mutants correspond to mutations inthe nrpd1 and nrpe1 subunits of these polymerases, respectively. Thestructure-based mutations were generated in the pSHH1::SHH1-3×Myc-BLRPconstruct using a QuikChange Site Directed Mutagenesis Kit (Stratagene)and were transformed into the shh1-1 mutant background via the floraldip method. siRNA-seq and ChIP-seq experiments in the Col and RdDMmutant lines were conducted using floral tissue and BS-seq experimentswere conducted using 10 day old seedlings. Southern and western blottingexperiments were conducted using tissue from the same individual plantlines in the T1 generation and using previously described probes(Johnson et al., 2008) and antibodies (Law et al., 2010). The siRNA-seqand BS-seq experiments in the SAWADEE domain point mutant lines wereconducted using floral tissue or 10 day old seedlings, respectively,from T3 plants homozygous for the various pSHH1::SHH1-3×Myc-BLRPtransgenes. The Pol IV ChIP experiments and co-immunoprecipitationexperiments in the various SAWADEE domain point mutant backgrounds wereconducted using floral tissue from F1 plants that were homozygous forthe shh1 mutant allele.

Results

To investigate the role of SHH1 in the RdDM pathway genome-wide, siRNAprofiles were generated in wild-type Col plants, shhl mutant plants, andseveral other RdDM mutants for comparison. In wild-type plants ˜12,500siRNA clusters were defined, representing 84.2% of all uniquely mapping24 nt siRNAs. Consistent with previous findings, 81.4% of these siRNAswere Pol-IV-dependent (Mosher et al., 2008; Zhang et al., 2007) (FIG.1A). Analysis of the siRNA clusters reduced in shhl mutants demonstratedthat SHH1 is a major regulator of siRNA levels, affecting 44% ofPol-IV-dependent clusters, which represents the majority of all 24 ntsiRNAs, including a majority of the clusters that were reduced in twodownstream RdDM mutants (drm2 and pol-v) (FIG. 1B). The overlap of thereduced siRNA clusters in these mutants formed four main subclasses(termed pol-iv only, shhl, shhl/drm2/pol-v, and drm2/pol-v; FIG. 1B),which were used for subsequent analyses. The clusters that depend solelyon Pol-IV were more enriched in pericentromeric heterochromatin thanthose that also depend on SHH1, DRM2, and Pol-V (FIG. 1C), suggestingthat different mechanisms may be controlling siRNA production in theeuchromatic arms verses pericentromeric heterochromatin.

In shhl mutants, siRNA levels at SHH1-dependent clusters (shhl andshhl/drm2/pol-v subclasses) were reduced to nearly zero, while siRNAlevels at SHH1-independent clusters experienced little to no change(FIG. 1D). These results demonstrate that SHH1 is a locus-specific RdDMcomponent that has strong affects at a large subset of RdDM loci.Notably, the two downstream RdDM mutants (drm2 and pol-v) have thestrongest effect on siRNAs levels at clusters that also require SHH1(shhl/drm2/pol-v subclass), and these same clusters are amongst thehighest siRNA producing clusters and correspond to the highest levels ofCHH methylation in the genome (Cokes et al., 2008)(FIG. 1D, 1E).Together, these findings suggest that SHH1, and the downstream RdDMmutants, are specifically converging to control siRNA levels at the mostactive sites of RdDM.

Using whole-genome bisulfite sequencing (BS-seq), we assessed DNAmethylation levels at the loci showing reduced siRNA levels and foundthat, consistent with its interaction with Pol-IV, SHH1 is an upstreamRdDM component; shhl mutants only affect DNA methylation at sites wheresiRNA levels are reduced (FIG. 1E). Furthermore, the residual siRNAspresent in shhl mutants appear to target some methylation, as predictedfor an upstream RdDM component. This is in contrast to the downstreammutants, drm2 and pol-v, which reduced DNA methylation to nearly pol-ivlevels even at sites that largely retain siRNAs (FIG. 1E), presumablydue to an inability to utilize siRNAs to target DNA methylation.

At loci corresponding to the shhl/drm2/pol-v and drm2/pol-v subclassesof siRNA clusters, the observed losses of siRNAs were accompanied with acorrespondingly large loss of DNA methylation (FIG. 1E). However, at thepol-iv only and shhl subclasses, large losses of siRNAs were accompaniedby relatively little DNA methylation loss. Without wishing to be boundby theory, it is believed that a likely explanation for this finding isthat other DNA methylation pathways are more active at sitescorresponding to the pol-iv only and shhl siRNA clusters. In addition tothe RdDM pathway, DNA methylation is controlled by two maintenancemethyltransferase pathways (Law and Jacobson, 2010): the DNAMETHYLTRANSFERASE 1 (MET1) pathway, which acts to maintain CGmethylation, and the CHROMOMETHYLTRANSFERASE 3 (CMT3) pathway, whichacts along with several H3K9 histone methyltransferases to maintain CHGand some CHH methylation (Cao et al., 2003). Consistent with this notionof methyltransferase redundancy, the pol-iv only and shhl subclasses ofreduced siRNA clusters displayed the highest levels of CMT3 occupancy(Du et al., 2012) (FIG. 1F), suggesting that in the absence of afunctional RdDM pathway the CMT3 pathway is able to maintain DNAmethylation at nearly wild-type levels at these loci. In contrast, theshh1/drm2/pol-v and drm2/pol-v subclasses, which show dramatic DNAmethylation losses in RdDM mutants, display lower levels of CMT3enrichment (FIG. 1F) and are more highly and precisely enriched for thePol-V polymerase (Zhong et al., 2012)(FIG. 1F, 1G), suggesting they areprimarily targeted by the RdDM pathway.

A genome-wide profile of Pol-IV occupancy in wild-type and shhl mutantbackgrounds was determined via chromatin immunoprecipitation of aFlag-tagged version of the largest Pol-IV subunit, NRPD1 (Law et al.,2011), followed by high throughput sequencing (ChIP-seq). Consistentwith the profile of Pol-IV-dependent siRNA clusters, Pol-IV was broadlyenriched at pericentromeric heterochromatin and at the definedsubclasses of siRNA clusters (FIG. 2A, 2B). In the shhl mutantbackground, Pol-IV levels were drastically reduced or eliminatedspecifically at shhl-dependent siRNA clusters (FIG. 2A), furthersupporting the biological relevance of the ChIP-seq profile andconfirming that the reduced-siRNA phenotype of shhl mutants is due toaltered Pol-IV chromatin association. At shhl-independent siRNA clustersPol-IV levels, like siRNA levels, were not reduced in an shhl mutant(FIG. 2A), suggesting that Pol-IV targeting to these loci requires analternative mechanism.

In addition to assessing the levels of Pol-IV enrichment over theaffected siRNA cluster subclasses, 928 reproducible, high confidencePol-IV peaks using multiple ChIP-seq datasets were defined. These peakswere enriched for siRNAs and DNA methylation and preferentiallyoverlapped with the high siRNA-producing shhl/drm2/pol-v or drm2/pol-vclusters as compared to the pol-iv only and shhl clusters (P<2.2e-16,Fisher's Exact Test), suggesting the ChIP procedure is preferentiallyidentifying sites where Pol-IV is most active. At the 928 defined Pol-IVpeaks, a variable level of SHH1-dependency was observed, promptingdivision of the peaks into three categories, SHH1-independent,SHH1-dependent, and SHH1-enhanced. In shhl mutants, DNA methylation andsiRNA levels were reduced at the SHH1-dependent sites and, to a lesserextent, at sites defined as SHH1-independent. However, siRNA and Pol-IVlevels were increased at SHH1-enhanced sites in shhl mutants, suggestinga redistribution of Pol-IV to these sites in shhl mutants. TheseSHH1-enhanced sites are unique amongst the Pol-IV peaks as they displayvery low levels of Pol-V enrichment, which could explain thecorrespondingly low level of CHH methylation observed at these sites inwild-type plants. Together with the analysis of SHH1-dependent siRNAclusters, these findings demonstrate that SHH1 plays a critical role infacilitating Pol-IV chromatin association at a subset of the most activesites of RdDM. SHH1 thus represents the first factor known to affect thetargeting of Pol-IV, controlling the initiation of RdDM.

To gain insight into the mechanism through which SHH1 facilitates Pol-IVtargeting, the function of its SAWADEE domain, a plant specific domainof unknown function (Mukherjee et al., 2009), was investigated. Sequencealignments of SHH1 proteins from diverse species are presented in FIG.10. The ability of the SAWADEE domain to bind modified histone tailsusing an Active Motif modified peptide array was tested. This assayrevealed that the SAWADEE domain has a preference for H3K9 methylation,but is also influenced by the methylation status of the H3K4 residue,with only unmodified or H3K4me1 modifications being tolerated. Toconfirm these results, isothermal calorimetry (ITC) experiments wereconducted using modified histone tail peptides (FIG. 3A, 3B). Theseanalyses revealed that the SAWADEE domain is quite unique in its abilityto bind all three H3K9 methylation states (me1, me2, and me3) with verysimilar affinity, K_(d)≈μM, which is approximately 17 fold higher thanobserved using unmodified H3 peptides (FIG. 3A). ITC experiments alsoconfirmed that while the SAWADEE domain will bind H3K9me2 peptides thatcontain H3K4me1 modifications, the presence of H3K4me2 or H3K4me3modifications resulted in reduced binding affinity. Finally, ITCexperiments using modified peptides corresponding to all other knownmethylated lysine residues on the N-terminal tails of the core histoneproteins confirmed the specificity of the SHH1 SAWADEE domain for H3K9methylation (FIG. 3B). Together, these binding studies demonstrate thatthe SAWADEE domain is a novel chromatin binding module that probes boththe K4 and K9 positions of the H3 tail and specifically binds repressiveH3K9 methyl-modifications.

Consistent with the observed in vitro binding specificity of the SHH1SAWADEE domain, SHH1-dependent Pol-IV ChIP-seq peaks are enriched forH3K9me2 (FIG. 3B). Pol-IV ChIP-seq peaks are depleted for H3K4methylation.

To determine the mode of methyl-lysine recognition by the SHH1 SAWADEEdomain, crystal structures of this domain either in the free-state or incomplex with modified H3 tails were solved (FIG. 3D). In the free-state,the SHH1 SAWADEE domain adopts a tandem Tudor domain-like fold thatcontains a unique zinc-binding motif located within the Tudor 2subdomain (FIG. 3D), making SHH1 the founding member of a new subclassof tandem Tudor domain folds (Bian et al., 2011). In this structure, azinc ion is coordinated by highly conserved cysteine and histidineresidues (Mukherjee et al., 2009). A DALI search indicated that theoverall structure of the SAWADEE domain resembles the UHRF1 tandem Tudordomain with an r.m.s.d. of 2.3 Å despite only sharing 11.8% sequenceidentity (Holm and Rosenstrom, 2010; Nady et al., 2011). This findingdemonstrates that although the sequence of the SAWADEE domain is plantspecific its fold is highly conserved in eukaryotic organisms.

The structures of the SHH1 SAWADEE domain in complexes with H3K9me1,H3K9me2 and H3K9me3 peptides were also solved and all three peptideswere bound in a similar manner. The 2.70 Å structure solved with anH3(1-15)K9me2 peptide (FIG. 4A) was further analyzed. This peptide bindswith directionality in a groove between the two Tudor subdomains,forming contacts with both subdomains (FIG. 4A, 4B, 4C). The free andH3K9me2-bound structures of the SAWADEE domain can be wellsuperpositioned (FIG. 4D) demonstrating that there is no significantconformational change in the SAWADEE domain upon ligand binding, afinding which differs from the situation reported for UHRF1 (Nady etal., 2011).

Within the SHH1 SAWADEE domain, there are two pockets that formintermolecular interactions with the unmodified K4 and the K9me2 sidechains of the bound peptide (FIG. 4E, 4F). The unmodified H3K4 sidechain inserts into an interfacial pocket formed by residues from boththe Tudor 1 and Tudor 2 subdomains. In this pocket, the K4 side chain isstabilized via intermolecular hydrogen bonds and electrostaticinteractions with the side chains of Glu130 and Asp141 (FIG. 4E). TheH3K9me2 side chain inserts into a hydrophobic aromatic cage formed byresidues of the Tudor 1 subdomain (FIG. 4F) where it is stabilized bycation-7r interactions in a manner similar to those reported previouslyfor methylated lysine-binding modules (Taverna et al., 2007). TheH3K9me3-SAWADEE and H3K9me1-SAWADEE complexes also position themethylated lysines within the same aromatic cage. Without wishing to bebound by theory, it is believed that the ability of the SAWADEE domainto bind equally against all three H3K9 methylation states may be wellexplained by structural observations: the methylated lysine recognitionaromatic cage can accommodate both H3K9me2 and H3K9me3 side chainsthrough common hydrophobic interactions with the aromatic cage,resulting in a lack of discrimination between these two methylationstates. In the H3K9me1 complex, although the lower lysine methylationstate has a decreased hydrophobic interaction with the aromatic cage,the side chain of His169 undergoes a small but significantconformational change in order to hydrogen bond with the K9me1 ammoniumproton, thereby contributing to the recovery of the binding affinity.This lack of specificity for the state of K9 methylation is in contrastto the higher level of methylation specificity observed for the tandemTudor domain of UHRF1, which has a slightly wider aromatic cage bindingpocket composed of a different combination of Phe and Tyr residues.Without wishing to be bound by theory, it is believed that this resultsin different shape complementarity requirements. The structural analysisindicates how very subtle changes in the tandem Tudor domain fold canresult in a fine tuning of methyl-lysine specificity.

The structure of the SAWADEE domain in a complex with anH3(1-15)K4me1K9me1 peptide was also solved. Overall, this structureresembles the structure with the H3K9me2 peptide, with the K4me1accommodated within the same K4 binding pocket. However, the methylgroup forms a stabilizing hydrophobic interaction with Leu201 in placeof the hydrogen bond that is formed between the ammonium proton of theunmethylated K4 and the Glu130 side chain (FIG. 4G). Since this K4binding pocket is relatively closed and narrow, higher methylationstates of K4 would likely introduce steric conflicts and/or disrupt allthe hydrogen bonding interactions. Without wishing to be bound bytheory, it is believed that this explains the observed decreases inbinding affinity.

To test the biological significance of methyl-H3K9 binding activityobserved for the SHH1 SAWADEE domain, point mutations were generatedwithin the two lysine binding pockets as well as the zinc binding motif.The impact of these mutations on DNA methylation, siRNA levels, andPol-IV recruitment in vivo were analyzed. Specifically, these pointmutations were engineered into an SHH1-3×Myc-BLRP-construct andtransformed into an shhl mutant background. DNA methylation levels wereassessed at a well characterized locus, MEA-ISR, by southern blottingand genome-wide by BS-seq experiments (FIG. 4H). Addition of a wild-typeSHH1-3×Myc-BLRP transgene restored DNA methylation, but constructsharboring mutations within the H3K9 or the H3K4 pockets were unable tofully complement the methylation defect observed in the shhl mutant(FIG. 4H) despite being expressed at levels comparable to the wild-typeSHH1-3×Myc-BLRP protein. Mutations in the zinc coordinating residuesresulted in nearly undetectable levels of protein and thus were notcharacterized further.

Similar to the shhl null mutant, the DNA methylation defects in the SHH1lysine binding pocket mutants is most pronounced in the shhl/drm2/pol-vsubclass of affected siRNA clusters (FIG. 4H) and consistent with theirpositions and predicted contributions to the binding affinity of theSHH1 SAWADEE domain, the F162AF165A and the D141A mutants displaystronger DNA methylation defects (FIG. 4H). In agreement with theobserved reductions in DNA methylation, assessment of siRNA levels inthe lysine binding pocket mutants via siRNA-seq experiments revealed asimilar pattern of defects with the F162AF165A and the D141A mutantsagain displaying a stronger phenotype (FIG. 4I). To determine whetherthe observed losses of siRNAs and DNA methylation reflect a defect inPol-IV activity at chromatin, Pol-IV ChIP experiments were conducted inthe SAWADEE domain point mutant backgrounds. All four point mutantsdisplayed reduced levels of Pol-IV occupancy in two biologicalreplicates (FIG. 4J). In addition, co-immunoprecipitation showed thatthe SHH1 SAWADEE domain point mutants were still able to interact withPol IV, demonstrating the interaction between SHH1 with the Pol IVcomplex in not dependent on its H3K9me binding activity. Together, thesefindings show that residues within both the K4 and K9 binding pocketsare critical for SHH1 function in vivo and demonstrate a role formethyl-H3K9 binding by SHH1 at the level of Pol IV association tochromatin.

It was found that the H3K4 binding pocket is important for SHH1 functionin vivo. The SHH1 SAWADEE does not bind H3K4 methylation in the absenceof H3K9 methylation and the addition of a methyl group to K4 does notimpart any additional binding affinity. Without wishing to be bound bytheory, it is believed that the mere presence of a lysine at theposition five residues back from the methylated H3K9 residue isnecessary for SAWADEE domain binding. Such dual lysine reading couldserve to help ensure that the SAWADEE domain only binds lysinemethylation when it is present at the K9 position of the H3 tail asopposed to a methylated lysine at a different position on the H3 tail oreven on a different histone or non-histone protein. ITC experiments wereconducted using H3 tails harboring an H3K4A mutation with or without thepresence of the H3K9me2 modification. The SAWADEE domain binds theH3K4AK9me2 peptide with approximately 30-fold weaker affinity than theH3K9me2 peptide. Furthermore, the SHH1 SAWADEE domain binds the H3K4Apeptide with weaker affinity than the wild type H3 tail, demonstratingthat the K4 residue is contributing to binding independent of themethylation status of the K9 residue.

Together, these in vivo and in vitro analyses demonstrate that the SHH1SAWADEE domain is probing the H3 tail at both the K4 and K9 positionsand is quite selective for the combination of histone modificationspresent at transposons and other repetitive DNA elements, namelyunmodified H3K4 and methylated H3K9. Although H3K9 methylation isanti-correlated with H3K4 methylation genome-wide (Zhang et al., 2009).Without wishing to be bound by theory, it is believed that the aversionof the SAWADEE domain to higher order H3K4 methylation could serve toallow transcription, which is correlated with H3K4 methylation, toovercome DNA methylation and associated repressive H3K9 methylmodifications in a developmental or locus specific manner. Likewise, thespecificity of the SAWADEE domain could inhibit siRNA generation at bodymethylated genes which contain CG methylation and H3K4methyl-modifications, but lack CHG and CHH methylation as well as siRNAs(Cokus et al., 2008; Zhang et al., 2009; Zhang et al., 2006).

In summary, it was demonstrated that SHH1 is a novel chromatin bindingprotein that functions in RdDM to enable Pol-IV recruitment and/orstability at the most actively targeted genomic loci in order to promotesiRNA biogenesis. Without wishing to be bound by theory, it is believedthat the finding that SHH1 binds to repressive histone modifications,together with the observation that SHH1 is required for Pol-IV chromatinassociation at a similar set of loci as downstream RdDM mutants, couldexplain the previously observed self-reinforcing loop in whichdownstream RdDM mutants are required for the production of full levelsof siRNAs from a subset of genomic loci (Zilberman et al., 2004; Xie etal., 2004; Li et al., 2006; Pontes et al., 2006) as it has been shownthat downstream RdDM mutants can cause a reduction of both DNAmethylation and H3K9 methylation at RdDM loci (Zilberman et al., 2003).

Example 2

The following Example relates to the characterization of the Arabidopsisthaliana proteins SUVH2 and SUVH9 and their involvement in promotingRNA-directed DNA methylation and gene silencing.

INTRODUCTION

Establishment of all DNA methylation and maintenance of much of thenon-CG methylation involves the RNA-directed DNA methylation (RdDM)pathway (Aufsatz et al., 2002; Pelissier and Wassenegger, 2000). Withoutwishing to be bound by theory, it is believed that there are two mainsteps in this pathway that are thought to target the DNAmethyltransferase, DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2)(Cao andJacobsen, 2002). The first upstream step involves the synthesis of 24nucleotide small interfering RNAs (siRNAs) by the concerted actions ofRNA POLYMERASE IV (Pol IV or NRPD), RNA-DIRECTED RNA POLYMERASE 2 (RDR2)and DICER-LIKE 3 (DCL3)(Pontier et al., 2005). The second downstreamstep involves the production of scaffold transcripts by RNA POLYMERASE V(Pol V or NRPE) with the help of the DDR complex (DRD1, a SWI/SNF2chromatin remodeler; DMS3, a chromosomal architectural protein; RDM1,unknown function). Without wishing to be bound by theory, it is thenbelieved that ARGONAUTE 4 (AGO4) loaded with a 24 nucleotide siRNA bindsto Pol V transcripts and, in an unknown fashion, acts to direct DRM2 toDNA for methylation (Law et al., 2010; Pikaard et al., 2008; Wierzbickiet al., 2009).

This Example demonstrates that Pol V transcription and its stablebinding to chromatin are dependent on SUVH2/SUVH9 genome-wide. These PolV binding sites are enriched in DNA methylation and, in many cases, withhistone H3K9 methylation. Furthermore, it is shown that tethering ofSUVH2 to the unmethylated epiallelefwa-4 results in the establishment ofDNA methylation and silencing of the FWA gene. This establishment ofmethylation coincides with recruitment of Pol V, but not with immediateenrichment of histone methylation, suggesting that histone methylationis secondary to the establishment of DNA methylation. A 2.4 Å crystalstructure of SUVH9 is also shown, thereby defining the folds andrelative orientations of the component domains in this family ofenzymes. A two-helix bundle near the N-terminus is positioned betweenand interacts with the SRA and pre-SET/SET domains. An incompletelyformed SAM cofactor-binding pocket, as well as the absence of a histonepeptide substrate-binding cleft within the structure of SUVH9, wasobserved, reflecting the absence of the post-SET domain in this enzyme.Without wishing to be bound by theory, it is believed that this mayexplain its lack of methyltransferase activity in vitro. These resultssuggest that SUVH2 and SUVH9 function in the recruitment of Pol V tochromatin, providing Pol V with a means to read epigenetic marks todirect its activity.

Materials and Methods

Biological Materials

All plants used were of the Arabidopsis thaliana Columbia (Col-0)accession, with WT referring to the parental strain. The nrpe1-12 T-DNA(SALK_033852), the suvh2suvh9 double, suvh4suvh5suvh6 triple mutantlines were described previously (Johnson et al., 2008; Pontier et al.,2005). NRPE1-FLAG transgenic plants (El-Shami et al., 2007) were crossedto suvh2suvh9 double mutant and homozygous F2 plants were identified.The fwa-4 epiallele was isolated from a met1 segregating population in aColumbia background.

Pol V Transcription and Chromatin Immunoprecipitation

Total RNA was isolated from flowers using TRIzol reagent (Invitrogen)and used to synthesize first strand cDNA using SuperScript III(Invitrogen). Real-Time PCR was performed using the SYBR Green SuperMix(Bio-Rad) in MxPro3000 qPCR machine (Stratagene) following themanufacturer instruction. ChIPs were done using 1-2 grams of 3-week oldplants or flowers and were either crosslinked in vivo or in vitro with1% formaldehyde as previously described (Zhong et al., 2012).Anti-H3K9me1 was obtained from Upstate (#07-450), anti-H3K9me2 wasobtained from Abcam (ab1220), and anti-NRPE1 was a gift from CraigPikaard.

Library Generation

Libraries for histone ChIP-seq were generated using paired-end regentsfrom NEB and adapters from the Illumina. Libraries for NRPE ChIP-seqwere generated using the NuGen multiplex kits. BS-seq libraries weregenerated as previously reported (Feng, 2011). All libraries weresequenced using the HiSeq 2000 platform following manufacturerinstructions (Illumina) at a length of 50 bp.

Alignment

Bisulfite-Seq and ChIP-seq reads were aligned to the TAIR8 version ofthe Arabidopsis thaliana reference genome using BS-seeker and bowtie,respectively, allowing for up to 2 mismatches. Only uniquely mappedreads were considered. ChIP-seq libraries were normalized such that alllibraries would contain an equal number of reads. NRPE1-Flag enrichmentover NRPE1 sites (Zhong et al., 2012) was normalized to Flag ChIP inColumbia (negative control). Histone methylation over NRPE sites wasnormalized to 80 sites determined to contain baseline levels of histonemethylation. These handpicked sites were in regions that were clearlymappable, but also had other characteristic marks of low histonemethylation, such as proximity to genes and low DNA methylation.

Zn Finger Constructs

The peptide containing 6 Zn fingers was designed as described in Segalet al (Segal et al., 2003) and cloned into pUC57 with Xho I sites atboth ends (Genewiz). This Xho I fragment was excised and inserted intothe unique Xho I site located in between the BLRP peptide and the HA tagin the pENTR-SUVH2 construct (Johnson et al., 2008), which encodes anHA-tagged SUVH2 driven by the endogenous SUVH2 promoter. This ZF-SUVH2was then recombined into JP726 (Johnson et al., 2008) and introducedinto fwa-4 using agrobacterium-mediated transformation. Transformedlines were selected for with BASTA.

Flowering Time

The flowering time of plants grown under short-day conditions wasdetermined by counting all rosette and cauline leaves up until theterminal flower. The average leaf number of between 20-30 plants wasdetermined.

Protein Preparation

The N-terminal truncated SUVH9 (residues 134-650) was cloned into apFastBacHT B vector (Invitrogen), which fuses a hexa-histidine tagfollowed by a TEV cleavage site to the N-terminus of target gene. Theplasmid was transformed into E. coli strain DH10Bac (Invitrogen) togenerate bacmid. Baculovirus was generated by transfecting Sf9 cellswith the bacmid following standard Bac-to-Bac protocol (Invitrogen). Theharvested virus was subsequently used to infect the suspended Hi5 cellfor recombinant protein expression. The recombinant protein was firstpurified using nickel affinity chromatography column (GE Healthcare).The hexa-histidine tag was cleaved by TEV protease. The target proteinwas further purified using a Q sepharose column and a Superdex G200 gelfiltration column (GE Healthcare). The purified protein was concentratedto 15 mg/ml and stored at −80° C.

Crystallization

Before crystal screening, the SUVH9 protein was mixed with the putativecofactor S-adenosyl-L-homocysteine (SAH) in a molar ratio of 1:3 or withSAH and a histone H3(1-15) peptide in a molar ratio of 1:3:3 at 4° C.for 2 hours. Crystallization of the SUVH9 was carried out at 20° C.using the hanging drop vapor diffusion method by mixing 1 μl proteinsample at a concentration of 11.5 mg/ml and 1 μl reservoir solution andequilibrating against 500 μl reservoir solution. SUVH9 was crystallizedin the condition of 0.2 M potassium thiocyanate, 0.1M Bis-Tris propanepH 7.5, and 20% PEG 3350 in free form, as well as in the presence of SAHor in the presence of SAH and H3(1-15) peptide. Square-shaped crystalsappeared in 2 weeks. All the crystals were dipped into reservoirsolution supplemented with 15% glycerol and flash cooled into liquidnitrogen for diffraction data collection. The diffraction data werecollected at beamline X29A, National Synchrotron Light Source (NSLS) atBrookhaven National Laboratory (BNL), New York at the zinc peakwavelength. The data were indexed, integrated, and further scaled withthe program HKL2000 (Otwinowski and Minor, 1997).

Structure Determination and Refinement

The structure of SUVH9 in the free state was solved usingsingle-wavelength anomalous dispersion method implemented in the programPhenix (Adams et al., 2010). The model building was carried out usingthe program Coot (Emsley et al., 2010) and structural refinement usingthe program Phenix (Adams et al., 2010). Throughout the refinement, afree R factor was calculated using 5% random chosen reflections. Thestereochemistry of the structural models were analyzed using the programProcheck (Laskowski et al., 1993). The data are indicative that crystalsof SUVH9 in presence of SAH and in the presence of SAH and H3(1-15)peptide are indeed the crystal of free form SUVH9. All the moleculargraphics were generated with the program Pymol (DeLano Scientific LLC).

Results

The synthesis of non-coding RNAs by Pol V is important to the downstreamstep in RdDM. To determine whether SUVH2/SUVH9 act before or after thesynthesis of these transcripts, Pol V transcription was assayed atseveral characterized sites (IGN22 and P6 shown in FIG. 5A)(Wierzbickiet al., 2008; Zhong et al., 2012). It was found that the double mutantsuvh2 suvh9 reduced Pol V transcripts to the same extent as the Pol Vmutant, nrpel (FIG. 5A). These results suggest that SUVH2/SUVH9 arerequired either for Pol V activity or its recruitment to chromatin.Using chromatin immunoprecipitations (ChIPs) of a Flag-tagged Pol V, itwas observed that only background levels of Pol V binding were found atIGN5 and IGN22 in the suvh2 suvh9 double mutant compared to a 6-foldenrichment in wild type (FIG. 5B). ChIP data was further analyzed bynext generation sequencing (ChIP-seq) and it was found that binding ofPol V at all previously identified sites (Zhong et al., 2012) wassignificantly decreased in a suvh2 suvh9 background (FIG. 5C, 5D).Therefore, SUVH2 and SUVH9 are required not only for Pol V activity, butalso for its stable association with chromatin.

To determine the level of DNA methylation at the Pol V binding sites invarious mutants, whole-genome bisulfite sequencing was performed. It wasfound that a suvh2 suvh9 mutant line reduced CHH methylation by 85%,which was close to the reduction in methylation measured in the nrpe1mutant line (FIG. 5E). These same mutant lines reduced CHG methylationby more than 50% underscoring that the RdDM pathway is also partlyresponsible for CHG methylation (Law and Jacobsen, 2010). These resultsdemonstrate that RNA-directed DNA methylation at Pol V sites genome-wideis dependent upon SUVH2 and SUVH9. It was found that the methylation atPol V sites was also partially dependent on the SUVH4/SUVH5/SUVH6/CMT3pathway, since the suvh4 suvh5 suvh6 triple mutant reduced CHGmethylation at Pol V sites by approximately 75% (FIG. 5E; similarreductions were observed with a cmt3 mutant).

As SUVH2/SUVH9 are in the same family of SET proteins asSUVH4/SUVH5/SUVH6, histone H3K9 methylation genome-wide by ChIP-seq wasanalyzed using antibodies specific for H3K9me1 and H3K9me2. A highcorrelation between non-CG DNA methylation and both H3K9me1 and H3K9me2was observed. The double mutant suvh2 suvh9 did not significantly affectthe levels of either H3K9me1 or H3K9me2 genome-wide, while the triplemutant suvh4 suvh5 suvh6 had a significant reduction in both H3K9me1 andH3K9me2. Both H3K9me1 and H3K9me2 over Pol V binding sites were mappedand it was found that both are enriched relative to the genome average,though H3K9me1 was found at higher levels than H3K9me2. H3K9me1 wasreduced in suvh4 suvh5 suvh6 triple mutant plants to background levelsat all Pol V sites, while the suvh2 suvh9 double mutant resulted insignificant losses of histone methylation (FIG. 5F). H3K9me2 was notsignificantly changed in any of the mutants.

Without wishing to be bound by theory, it is believed that while thelosses observed in the suvh2 suvh9 double mutant may be direct, butseveral lines of evidence support that these decreases in histonemethylation are a secondary consequence of reduced DNA methylation.First, at some sites, H3K9me1 is part of a larger patch ofheterochromatin and unaffected by suvh2 suvh9 while at others both DNAmethylation and H3K9me1 is lost. Furthermore, a third class of sites wasfound with no detectable H3K9me1, but which had SUVH2/SUVH9 dependentDNA methylation. Second, a similar decrease of histone methylation wasobserved at these same sites in another RdDM mutant, rdr2. Thus it islikely that SUVH2/SUVH9 function to recruit Pol V resulting in RdDM,which then recruits the active histone methyltransferases SUVH4, SUVH5and SUVH6. These enzymes bind methylated DNA through their SRA domainsand methylate the associated histones. Without wishing to be bound bytheory, it is believed that it is most likely that the losses of H3K9methylation in suvh2 suvh9 double mutants is an indirect consequence ofthe loss of RNA directed DNA methylation.

To test directly whether the action of SUVH2/SUVH9 may be sufficient totarget RNA-directed DNA methylation, a specific zinc finger (ZF) totether SUVH2 to an unmethylated epiallele of FWA, fwa-4 (fwa-4 is theunmethylated FWA epiallele in Columbia, fwa-1 is the unmethylatedepiallele in the Landsberg erecta ecotype) was engineered. The FWA geneencodes a homeodomain transcription factor that is normally silenced dueto DNA methylation in its promoter (Soppe et al., 2000). The FWAepiallele has lost all DNA methylation, leading to ectopic expression ofFWA and a heritable late flowering (Kakutani, 1997; Soppe et al., 2000).siRNAs normally involved in targeting DNA methylation still exist in theFWA epiallele but seem unable to direct downstream factors to methylatethe promoter (Chan et al., 2006). Without wishing to be bound by theory,it is believed that in one model that although siRNAs are present, thePol V scaffold transcript it missing. The FWA promoter region containstwo small direct repeats followed by two larger repeats (Kinoshita etal., 2007). A peptide containing six ZFs was designed to recognize asequence found in each of two small repeats (CGGAAAGATGTATGGGCT)(SEQ IDNO: 141)(Kolb et al., 2005; Segal et al., 2003). The coding region forthis peptide was then inserted into a HA-tagged SUVH2 transgene drivenby the endogenous SUVH2 promoter (ZF-SUVH2) and introduced into an fwa-4line using Agrobacterium-mediated transformation (FIG. 6A).

In T1 plants, approximately 75% of the ZF-SUVH2 transformants floweredearly as compared to the parental fwa-4 line. Transformants of thecontrol HA-tagged SUVH2 (HA-SUVH2) line that did not contain the Znfinger flowered at the same time as the fwa-4 parent, showing that theeffect was specific to the ZF-SUVH2 fusion. T1 plants containing eitherthe ZF-SUVH2 or HA-SUVH2 were carried out to the T2 generation andflowering time was determined (FIG. 6A, 6B). The line containingZF-SUVH2 flowered just slightly later than the Columbia (WT) control,whereas HA-SUVH2 without a Zn finger flowered at about the same time asthe fwa-4 parent. These results suggest that ZF-SUVH2 is in fact beingtargeted to the FWA promoter and causing transcriptional repression.

DNA methylation in the FWA promoter region was analyzed using bisulfitesequencing. In the wild-type line a large region of DNA methylation isdetected, with particularly high levels of CG methylation (FIG. 6D). Infwa-4, this region was completely devoid of DNA methylation. In threeindependent T1 lines containing the ZF-SUVH2 in fwa-4, a methylationprofile that was distinct from WT was observed. DNA methylation was at ahigh level immediately around the Zn finger binding sites in all threesequence contexts. DNA methylation then tapered off over the downstreamtranscribed region (FIG. 6E). In the control HA-SUVH2 T1 plants, no DNAmethylation was observed at FWA. These results indicate that targetingSUVH2 to FWA with the ZF is sufficient to induce DNA methylation andgene silencing.

To determine whether Pol V was present at FWA in the fwa-4 epimutant,endogenous antibodies to NRPE1 were used in ChIP experiments of wildtype, nrpe1 and fwa-4 lines. Enrichment of Pol V at two known Pol Vsites, IGN5 and IGN22, was observed in the wild type and fwa-4 lines,but not in nrpe1 mutant plants (FIG. 7A). When the FWA locus wasexamined, enrichment in the wild type at both the promoter andtranscript regions was observed, but not in nrpe1 or fwa-4 (FIG. 7A).Thus, Pol V is present at the FWA locus when it is in its DNA methylatedand silent state in the wild type, but not when it is in an unmethylatedstate in the fwa-4 epiallele. To determine if binding of the ZF-SUVH2 tothe FWA promoter recruits Pol V, NRPE1 ChIP in a T2 line containingZF-SUVH2 in fwa-4 was performed. Unlike the parental fwa-4 line, in thepresence of ZF-SUVH2, an enrichment of Pol V at FWA was observed (FIG.7A), indicating that ZF-SUVH2 targeting acted to recruit or stabilizePol V at FWA.

The histone methylation status of TWA in the different lines was alsoassayed. In the wild-type line, a slight enrichment of H3K9me1 in theFWA promoter region and a 4-fold enrichment in the FWA transcript regionwas observed (FIG. 7B). In the fwa-4 line, no enrichment was observed.No enrichment of H3K9me1 in early flowering ZF-SUVH2/fwa-4 T1 plants wasdetected (FIG. 7B). However, in the next generation from these plants(T2), a slight enrichment of H3K9me1 was observed, slightly strongerover the promoter region than the transcript region (FIG. 7C). Theseresults suggest that although ZF-SUVH2 recruits Pol V and DNAmethylation immediately in the first generation, histone methylation isnot immediately restored, but accumulates after the plants are inbredfor an additional generation.

To gain additional insights into the function of SUVH2/SUVH9 astructural analysis of both proteins was performed. Through proteincrystallization, the structure of an N-terminally-truncated SUVH9construct (residues 134-650) that represents the first structural viewof the Arabidopsis SUVH family SRA-SET cassette-containing proteins wassolved. The first 130 residues of SUVH9 are predicted to be disorderedand without homology to any known domains, while the remaining residuescontain all the known functional domains of SUVH9 (the SRA, pre-SET, andSET domains) (FIG. 8A). The structure of SUVH9 was determined using thesingle-wavelength anomalous dispersion method and refined to 2.4 Åresolution with an R factor of 18.7% and an R free of 22.3% (FIG. 8B).The structure of SUVH9 is composed of three segments: a two-helix bundletowards the N-terminus (residues 138-194), the SRA domain (residues195-379), and the pre-SET/SET domains (residues 380-637) (FIG. 8B).

A unique feature of the SUVH9 structure is the formation and location ofa two-helix bundle towards the N-terminus, which is sandwiched betweenthe SRA domain and the pre-SET/SET domains, thereby interacting withboth of them. The interface between the two α-helices is enriched withhydrophobic residues, which participate in extensive van der Waalsinteractions, supplemented by salt bridge formation following insertionof Glu166 of the longer first helix between Arg178 and Lys182 of theshorter second helix (FIG. 8C). These hydrophobic interactions and saltbridges stabilize the relative position of the two helices, and serve asa scaffold for anchoring of the SRA domain and pre-SET/SET domains oneither side of the two-helix bundle, thereby resulting in the formationof an overall rigid topology for the entire protein.

The two-helix bundle is deeply buried at the interface of the SRA domainand pre-SET/SET domains, whose relative alignments are stabilizedthrough formation of extensive hydrophobic and hydrophilic interactions.The longer first helix (residues 138-169) of the two-helix bundleinserts into the interface between the SRA and the pre-SET/SET domains.The N-terminal segment of the longer helix is very hydrophilic and makesseveral pairs of salt bridges and hydrogen bonds with surroundingresidues (FIG. 8D). By contrast, the C-terminal part of this helixcontains a large and continuously hydrophobic surface that interactswith both the shorter second helix (FIG. 8C) and other domains of theprotein (FIG. 8E). A long loop extends out from the SET domain (FIG. 8E)and covers the outer surface of the longer helix. The tip of this loopcontains several hydrophobic residues (Leu559, Va1562, and Leu563) thatform extensive van der Waals interactions with hydrophobic residues(Ile154, Leu158, Phe161, and Leu162) on one face of the longer helix.Without wishing to be bound by theory, it is believed that the longerhelical segment might play an important role in the stabilization of theoverall architecture of the SUVH9 protein. The shorter second helixmainly interacts with the C-terminal part of the longer helix (FIG. 8B,8C), supplemented by few hydrogen bonding and hydrophobic interactionswith the SRA domain (FIG. 8F).

The SRA domain of SUVH9 resembles the reported structures of SRA domainsfrom UHRF1 and SUVH5 (Arita et al., 2008; Avvakumov et al., 2008;Hashimoto et al., 2008; Rajakumara et al., 2011). The superposition ofSUVH9 and SUVH5 SRA domains yields an RMSD of 1.2 Å for 145 aligned Caatoms, consistent with almost identical folding of the two proteins,whose core elements are composed of a six-stranded twisted β-barrel andtwo α-helices. Unlike the observed disordered loop in SUVH5 SRA domain,the C-terminus of the SUVH9 SRA domain forms an α-helix, that isfollowed by a short turn and then directly links to the pre-SET domain.

The relative orientation between the SRA and pre-SET/SET domains isstabilized by extensive direct interactions between them and throughinteractions with the two-helix bundle. The direct interaction betweenthe SRA domain and the pre-SET/SET domains are mainly dominated byhydrophobic interactions (FIG. 8G). In particular, the C-terminalextended α-helix of the SRA domain uses a hydrophobic surface tointeract with a continuous hydrophobic surface of the pre-SET/SETdomains, with residues flanking the α-helix of the SRA domain alsocontributing to the formation of the hydrophobic interface. Thestructure of the pre-SET/SET domains of SUVH9 is similar to thepublished structures of H3K9 histone methyltransferases, such as Dim5,G9a, and GLP (Wu et al., 2010; Zhang et al., 2002; Zhang et al., 2003).Superposition of the pre-SET/SET domains of SUVH9 and human H3K9methyltransferase GLP yields an RMSD of 1.8 Å for 252 aligned Ca atomS,although they only share a sequence identity of 34%. As commonlyobserved in other SET domain proteins, nine conserved Cys residues ofthe pre-SET domain of SUVH9 coordinate three Zn²⁺ions to form anequilateral triangle cluster (FIG. 8B).

Although SUVH9 contains histone methyltransferase like pre-SET and SETdomains, it exhibits neither detectable histone methyltransferaseactivity, nor binding capacity for SAM cofactor in vitro (Johnson etal., 2008). In the primary sequence, although SUVH9 retains two Tyrresidues (Tyr522 and Tyr636, which correspond to Tyr1124 and Tyr1211 ofhuman GLP, that contribute to methyltransferase activity (Wu et al.,2010; Zhang et al., 2002; Zhang et al., 2003), it lacks the post-SETdomain, which is important for cofactor and peptide substrate binding,as well as catalysis. The pre-SET and SET domains of human GLP and SUVH9adopt similar folding topologies (Wu et al., 2010). In human GLP, theSAH binding pocket is relatively narrow and exhibits pronouncedstructural and chemical complementarity for SAH (FIG. 9A). Moreover, theexistence of a post-SET domain with the capacity to cover the adeninemoiety of SAH acts to stabilize the binding of this cofactor molecule.By contrast, the putative SAH-binding pocket of SUVH9 is very open (FIG.9B) and cannot retain a bound SAH molecule, especially in the absence ofthe stabilizing role of the post-SET domain. In addition, usually SUVfamily active methyltransferases utilize a Cys residue from the SETdomain together with three Cys residues from the post-SET domain tocoordinate a Zn²⁺ ion to stabilize the relative position andconformation of the loop-enriched region of the post-SET domain. Bycontrast, the Cys residue is replaced by a Thr in the SET domain ofSUVH9, so that even if a partner protein were to bring three Cysresidues, it would still not be possible to form a Zn²⁺ stabilizedcoordination center.

In SET domain-containing H3K9 methyltransferases, the peptide substrateis positioned between the SET and post-SET domains (FIG. 9C), andstabilized through formation of extensive main chain and side chainintermolecular interactions with the enzyme. In human H3K9methyltransferase GLP, an acidic loop region (residues 1145-1153) of theSET domain is involved in the recognition of the peptide substrate (FIG.9C). By contrast, the corresponding segment in SUHV9 contains aninsertion loop of 25 residues, enriched with hydrophobic residues (FIG.8H). The insertion loop adopts a well-defined topology because it isstabilized through formation of extensive hydrophobic interactions withresidues from the SET and pre-SET domains (FIG. 8H), especially the tipof the loop, which covers and interacts extensively with the two- helixbundle (FIG. 8H). An examination of the SUVH9 structure identifies thepotential for steric clash between the insertion loop and a putativelybound peptide substrate, thereby preventing access of the peptidesubstrate into the peptide-binding cleft of the SUVH9 protein (FIG. 9D).

This Example demonstrates that SUVH2 and SUVH9 are required for therecruitment of Pol V to regions containing DNA methylation. Furthermore,a ZF-SUVH2 fusion was used to show that SUVH2 targeting is sufficientfor recruitment of Pol V and DNA methylation to an unmethylated targetgene. Without wising to be bound by theory, it is believed that themechanism of action of SUVH2 and SUVH9 provides a reinforcing loopbetween pre-existing DNA methylation and further rounds of RNA-directedDNA methylation.

Example 3

The following Example relates to the production and characterization ofa modified A. thaliana SHH1 protein that is engineered to contain anucleic acid binding domain to target the modified SHH1 protein to aspecific nucleic acid sequence. In this example the targeting of SHH1 tothe promoter regions of the APETALA1 locus was associated with theenrichment of siRNAs at APETALA1.

Materials and Methods

Construction of TAL-SHH1

The Gateway entry clone containing SHH1 including 1.4 kb of the promoterregion and the ORF with C-terminal BLRP and 3×Myc tags was describedpreviously (Law et al., 2011). BsaI recognition sites were removed fromthe SHH1 entry clone by site directed mutagenesis (Quickchange II,Agilent) using primers SHH1deltaBsaLfo,5′-GGGAGAGTGAACGTTGGTGACCTGCTTCTATGTTT-3′ (SEQ ID NO: 142),SHH1deltaBsaLre and 5′-AAACATAGAAGCAGGTCACCAACGTTCACTCTCCC-3′ (SEQ IDNO: 143). After removing the BsaI sites the entry clone was linearizedby restriction digestions with XhoI. In order to insert the DNA sequenceencoding a modified Hax3-based transcription activator-like effector(TALE) (Sanjana et al., 2012) excluding the C-terminal nuclearlocalization signal and acidic activation domain flanked by GSSGSSlinkers in frame in between the C-terminal BLRP and 3×Myc tags of SHH1,2.8 kb of the TALE backbone including the ccdB selection cassette wereamplified from TALE transcriptional activator (TALE-TF) plasmid(Addgene) using primers TALETFintotag_fo,5′-CCAAGGACCTCTCGAGGGATCTTCAGGTTCATCTTCGCGGACCCGGCTCCCT-3′ (SEQ ID NO:144) and TALETFintoSHH1Myc_re,5′-CATAGATCCCTCGAGTGAAGAACCAGATGATCCGCTAGCTGACGCGCGA-3′ (SEQ ID NO:145). The amplification product was fused with the linearized entryclone using In-Fusion HD cloning system (Clontech). The TALE DNA-bindingdomain targeting the sequence 5′-TTAGGATTTGCGTGTCGAC-3′ (SEQ ID NO: 146)corresponding to chromosome 1 from nucleotide positions 25986363 to25986381 in the promoter region of APETALA1 (AT1G69120) was assembledfrom 18 monomer-repeats (Addgene) by Golden Gate cloning and insertedbetween the BsaI sites flanking the ccdB selection cassette (Sanjana etal., 2012). The DNA sequence encoding the TALE target repeats is listed(SEQ ID NO: 140). In order to facilitate binding of the TAL-SHH1 fusionprotein to methylated cytosine the repeat variable “diresidue” (RVD) N*was used (Valton et al., 2012). Plasmids encoding monomer RVDs N* and NHwere generated by site-directed mutagenesis (Quickchange II, Agilent) ofthe TALE monomer template plasmid pNN_v2 (Addgene) using primersNN>N*_fo, 5′-GTGGCAATTGCGAGCAACGGGGGAAAGCAG-3′ (SEQ ID NO: 147),NN>N*_re, 5′-CTGCTTTCCCCCGTTGCTCGCAATTGCCAC-3′ (SEQ ID NO: 148),NN>NH_fo, 5′-GGCAATTGCGAGCAACCATGGGGGAAAGCAGGCAC-3′ (SEQ ID NO: 149) andNN>NH_re, 5′-GTGCCTGCTTTCCCCCATGGTTGCTCGCAATTGCC-3′ (SEQ ID NO: 150),respectively. TALE-TF plasmid encoding RVD N* was generated bysite-directed mutagenesis (Quickchange II, Agilent) of pTALE-TF_v2 (NN)(Addgene) using primers TALETF_NN>N*_fo,5′-TGGCTATTGCATCCAACGGGGGCAGACC-3′ (SEQ ID NO: 151) and TALETF_NN>N*_re,5′-GGTCTGCCCCCGTTGGATGCAATAGCCA-3′ (SEQ ID NO: 152). Binary vector wasgenerated using LR clonase II (Life Technologies) and modifiedpEarlyGate302 destination vectors containing the hph selection marker(Law et al., 2011).

Plant Material

TAL-SHH1 constructs were transformed into shhl (SALK_074540) of ecotypeCol-0 by Agrobacterium tumefaciens strain ABLO using the floral dipmethod (Clough and Bent, 1998). T1 plants were selected with HygromycinB and expression of the chimeric TAL-SHH1 proteins was tested by proteinisolation and Western blot with antibodies against the 3×Myc,respectively. T1 plants showing strong transgene expression wereselected.

Results

After selecting a plant containing the TAL-SHH1 directed against theAPETALA1 gene, small RNA libraries were generated and deeply sequencedusing established protocols (Law et al., 2013) to detect the presence ofsmall RNAs produced at the APETALA1 gene in response to targeting SHH1to the promoter. As a control, small RNAs were sequenced from a wildtype plant, which would not be predicted to contain siRNAs present inthe promoter region of APETALA1. As shown in FIG. 18, small RNAs weredetected corresponding to both strands of the DNA in the TAL-SHH1 plantsbut not the wild type plants, indicating that the modified SHH1 proteincould target small RNAs to the AP1 promoter.

Example 4

The following Example highlights the relationship between DNAmethylation and Pol V binding via SUVH2/SUVH9 and demonstrates thatSUVH2 interacts with DRD1.

Materials and Methods

Experimental Procedures in Arabidopsis

Chromatin immunoprecipitations (ChIPs) were performed as inBernatavichute et al. (2008), except that ground tissue was crosslinkedwith formaldehyde in the following buffer: 10 mM HEPES pH 8.0, 1 MSucrose, 5 mM KCl, 5 mM MgCl2, 5 mM EDTA, and 0.6% Triton X-100. Allprimers used are listed in Table 12 below. Libraries for NRPE1 ChIP-Seqwere generated using the Ovation Ultralow DR Multiplex System (NuGen).Bisulfite sequencing followed by PCR amplification and cloning of FWAfragments was done using EZ DNA Methylation-Gold kit (Zymo Research) asperformed in Johnson et al. (2008). BS-Seq libraries were generated asdescribed in Example 1, and all libraries were sequenced using the HiSeq2000 platform following manufacturer instructions (Illumina) at a lengthof 50 bp. Zinc finger constructs were generated as described in Example2.

TABLE 12 List of Primers Primer Primer sequences numbers from 5′ to 3′Actin JP2699 AGCACGGATCGAATCACATA (SEQ ID NO: 153) JP2700CTCGCTGCTTCTCGAATCTT (SEQ ID NO: 154) IGN22 JP9978 CGGGTCCTTGGACTCCTGAT(SEQ ID NO: 155) JP9979 TCGTGACCGGAATAATTAAATGG (SEQ ID NO: 156) P6JP10059 GGCTTCGATAGGAAGAATGCCC (SEQ ID NO: 157) JP10060GTGAAACTGCCAGATCCAAATTC (SEQ ID NO: 158) IGN5 JP6606TCCCGAGAAGAGTAGAACAAATGCTAAAA (SEQ ID NO: 159) JP6607CTGAGGTATTCCATAGCCCCTGATCC (SEQ ID NO: 160) Ta3 JP2456TGGAATCTCAGGGTCAAGG (SEQ ID NO: 161) JP2457 CCTTCTGAGGTGAGGGACA(SEQ ID NO: 162) FWAp JP7717 AAGAGTTATGGGCCGAAGC (SEQ ID NO: 163) JP7718CGCTCGTATGAATGTTGAATG (SEQ ID NO: 164) FWAt JP6747 ATAAAGAGCGGCGCAAGAT(SEQ ID NO: 165) JP6748 CGCTCTAGGGTTTTTGCTTT (SEQ ID NO: 166) Neg JP3034AGGCCCCATCTCACAAATAC control (SEQ ID NO: 167) Neg JP3035GTCGCCAGGTAGATTTGGTT control (SEQ ID NO: 168)

Data Analysis

Bisulfite-Seq (BS-Seq) reads were aligned to the TAIR10 version of theArabidopsis thaliana reference genome using BS-seeker. For BS-Seq up to2 mismatches were allowed and only uniquely mapped reads were used.

Co-Immunoprecipitation Experiments

Nicotiana benthamiana was infiltrated with pLJ322 (ZF-HA-SUVH2 inJP7468) and leaves were collected after 3 days. Leaves that were notinfiltrated were used as a negative control. 3 g of tissue was ground inliquid N2 and resuspended in 12 ml of IP buffer (50 mM Tris pH 8.0, 150mM NaCl, 5 mM MgCl2, 10% glycerol, and 0.1% NP40) with 1 μg/mlpepstatin, 1 mM PMSF, and 1× complete protease inhibitor tab-EDTA(Roche). The extracts were filtered through miracloth and centrifugedfor 5 min at 3,000 g. 200 μl HA-magnetic beads (MRL) were added androtated at 4° C. for 45 mM. After 3 washes with IP buffer, these werethen incubated with DRD1-Flag Arabidopsis flower extracts made in thesame fashion. Incubation continued for 45 mM rotating at 4° C. The beadswere washed 3 times with IP buffer and boiled in 60 μl SDS dyes. Westernblots were probed with either anti-Flag-HRP or anti-HA-HRP antibodies.The co-IP experiment in Arabidopsis was performed starting with 2 g offlowers from plants expressing HA-SUVH2, Flag-DRD1 or T2 plantscontaining both HA-SUVH2 and Flag-DRD1. Extracts were made as describedabove and 100 μl of Flag-magnetic beads (Sigma) were added and incubatedwith rotation at 4° C. for 45 min. Washes and western blots wereperformed as described above.

Results

The results presented in Example 2 illustrate how a SUVH protein fusedto DNA-binding domain motifs can be targeted to an unmethylated targetgene and recruit Pol V and DNA methylation to the unmethylated targetgene. Sequences alignments of various SUVH proteins are presented inFIG. 11. Example 2 also establishes that SUVH2 and SUVH9 are requirednot only for Pol V activity, but also for its stable association withchromatin throughout the genome.

To determine the effect of SUVH2 and SUVH9 on DNA methylation at definedPol V binding sites, whole-genome bisulfite sequencing (BS-Seq) wasutilized, as seen in Example 2. BS-Seq results of the single mutantssuvh2 and suvh9 was also analyzed to determine if SUVH2/SUVH9 actredundantly at all sites or have non-overlapping sites where theyfunction. It was found that suvh2 had a stronger effect than suvh9 atPol V sites as well as at differentially methylated regions (DMRs)defined in either suvh2 or suvh9 single mutants, or in the suvh2 suvh9double mutant (FIG. 12). These results indicate that SUVH2 and SUVH9 actredundantly throughout the genome to control RNA-directed DNAmethylation.

Without wishing to be bound by theory, the results presented in Example2 also suggest that a reinforcing loop exists between DNA methylationand Pol V binding via SUVH2/SUVH9. To further investigate this, amutation in the maintenance methyltransferase METI that eliminates CGmethylation genome-wide and also reduces CHG and CHH methylation(Aufsatz et al., 2004; Stroud et al., 2013; Lister et al., 2008) wasutilized (FIG. 13B). Using endogenous antibodies to NRPE1, ChIP-seqrevealed that Pol V occupancy was virtually eliminated in met1 comparedto wild type at sites normally occupied by Pol V (FIG. 13C). Incontrast, at a series of sites previously identified as gainingmethylation in met1 (Stroud et al., 2013), an increase in Pol V bindingwas observed (FIG. 13D and FIG. 13E). These results suggest that DNAmethylation is an important component of Pol V recruitment. Pointmutations in the SRA domains of both SUVH2 and SUVH9 were shown to causea loss of RNA-directed DNA methylation, indicating that the SRA domainscontribute to function (Johnson et al., 2008). Together, and withoutwishing to be bound by theory, these results suggest that SUVH2/SUVH9binding to methylated DNA recruits Pol V, thus providing a link betweenpreexisting DNA methylation and the recruitment of further methylationby the RdDM pathway.

It was further found that a KYP protein fused to a zinc finger targetingFWA in an fwa-4 background (ZF-KYP/fwa-4) flowered with similar timingto the fwa-4 mutant (late flowering compared to wild-type), in contrastto the results observed for ZF-SUVH2/fwa-4 plant lines. ZF-KYP wasincluded as an additional negative control because KYP (also known asSUVH4), is a SUVH protein not required for RdDM. The presence of thecontrol ZF-KYP at FWA was also shown by ChIP (FIG. 15A).

To further investigate this targeting, using the plant lines asdescribed in FIG. 6 from Example 2, bisulfite sequencing was used todetermine if FWA gene silencing was associated with DNA methylation. Inthe wild-type line a large region of DNA methylation is detected, withparticularly high levels of CG methylation (FIG. 14A). In both fwa-4 andtransformants with ZF-KYP or HA-SUVH2, this region was completely devoidof DNA methylation (see ZF-KYP; FIG. 14A). In three independent T1 linesanalyzed containing the ZF-SUVH2 in fwa-4, DNA methylation at a highlevel immediately around the Zn finger binding sites in all cytosinesequence contexts was observed, which then tapered off over thedownstream transcribed region (Example 2, FIG. 6E). One of the lines wasfollowed (ZF-SUVH2-2) out to the T2 and T3 generations, and BS-seq wasused to determine the extent of methylation spreading (FIG. 14A). It wasfound that methylation extended approximately 150 base pairs in eitherdirection from the binding sites and did not expand significantlybetween generations. It was also observed that this DNA methylation andsilencing was maintained in T2 segregants that had lost the ZF-SUVH2transgene (FIG. 15B). These results indicate that targeting SUVH2 to FWAis sufficient to induce DNA methylation and gene silencing, and thatthis epigenetic silent state can be maintained in the absence ofZF-SUVH2.

From Example 2, experiments were designed to test whether the ZF-SUVH2was recruiting Pol V. NRPE1 ChIP was used to examine the levels of Pol Vat FWA in wild-type, nrpe1, and fwa-4 lines. Enrichment of Pol V at twoknown Pol V sites, IGN5 and IGN22, in the wild-type and fwa-4 lines, butnot in nrpe1 mutant plants was observed (FIG. 7A). At FWA, enrichment ofPol V in the wild type at both the promoter and transcript regions, butnot in nrpe1 or fwa-4 was observed (FIG. 7A). Thus, Pol V is present atFWA in its DNA methylated and silent state in the wild type, but not inits unmethylated state in the fwa-4 epiallele. To determine if bindingof the ZF-SUVH2 to TWA recruits Pol V, NRPE1 ChIP was performed in a T2line containing ZF-SUVH2 in fwa-4. Unlike the parental fwa-4 line, theZF-SUVH2 line showed enrichment of Pol V at FWA (FIG. 7A). Together,these results indicate that SUVH2 is sufficient to localize Pol V at theFWA promoter, leading to DNA methylation and gene silencing.

In order to address the potential mechanism by which SUVH2 or SUVH9target RdDM, mass spectrometry datasets generated by immunoprecipitatingprotein complexes utilizing various epitope-tagged RdDM factors werequeried. Although SUVH2/9 peptides in several IP-mass spectrometrystudies from purification of Pol V (utilizing NRPE1-Flag) have not beenobserved, SUVH2 peptides in two independent mass spectrometric datasetsfor DRD1 (FIG. 16) were identified. DRD1 is a component of the DDRcomplex (also containing DMS3 and RDM1) which interacts with Pol V (Lawet al., 2010) and is required for Pol V occupancy throughout the genome(Zhong et al., 2012). The number of SUVH2 peptides observed was lowerthan those from the DMS3 and RDM1 proteins which are stoichiometriccomponents of the DDR complex, and also lower than the level of peptidesof most Pol V complex components, suggesting that the interactionbetween SU V H2 and DRD1 is weaker or more transient than theinteraction between the DDR components or between DDR and Pol V. Toconfirm the interaction between DRD1 and SUVH2, epitope-tagged SUVH2 wasexpressed in leaves of Nicotiana benthamiana and purified on HA magneticbeads. Using this as a source of SUVH2, DRD1-Flag was specifically andreproducibly pulled down from transgenic Arabidopsis protein extracts(FIG. 14B: beads-SUVH2). As a negative control, the same assay wasperformed using N. benthamiana that was not expressing tagged SUVH2, andDRD1-Flag could not be detected in this assay (FIG. 14B: beads-mock). Inaddition, co-immunoprecipitation experiments were performed withHA-tagged SUVH2 and Flag-tagged DRD1 in transgenic Arabidopsis plantsand an interaction between these proteins was also observed (FIG. 15C).These results confirm the IP-mass spectrometry observations and, withoutwishing to be bound by theory, are consistent with a model in whichSUVH2 acts indirectly via a transient interaction with DDR complexcomponents including DRD1 to recruit Pol V.

Example 5

This Example demonstrates the targeting of different components of theRNA-directed DNA methylation pathway to recruit Pol V to specific loci.

INTRODUCTION

The RNA-directed DNA methylation (RdDM) pathway mediates de novo DNAmethylation in plants. Examples 2 and 4 demonstrate the use of ZF-SUVH2to specifically target methylation and silencing of a target locus. Thiswas achieved by utilizing the FWA gene as a target. Expression of FWAcauses a strong late-flowering phenotype in Arabidopsis. Methylation atthe promoter of this gene, as is present in wild-type plants, causestranscriptional silencing of FWA and results in an early-floweringphenotype relative to fwa-4 mutants. The fwa-4 Arabidopsis epigeneticmutant shows no methylation in the promoter of the FWA gene and thusshows the characteristic late-flowering phenotype (relative to wildtype). Examples 2 and 4 describe a chimeric SUVH2 protein fused to aZinc Finger (ZF) protein designed to target the promoter of FWA inArabidopsis, ZF108, and demonstrates that this fusion protein canpromote methylation at this genomic site in fwa-4 plants. Thismethylation targeting is accompanied by the recruitment of Pol V to this(FWA) site and results in the production of the non-coding RNA needed totrigger methylation, gene silencing, and therefore produce anearly-flowering phenotype.

Materials and Methods

Fusion Protein Construction

In order to create the different fusion proteins described in thisexample, the ZF108 fragment in the pUC57 plasmid described in Example 2was digested with the restriction enzyme XhoI and inserted directly intothe unique XhoI site in different genes, or inserted into a pCR2 plasmidcontaining either Flag-BLRP or HA-BLRP fusions that contain an XhoI sitelocated in between the tag and BLRP and that are flanked by AscIrestriction sites. Individual constructs were constructed as describedbelow.

DRD1-HA-ZF: The HA-ZF108-BLRP fusion in the pCR2 plasmid was digestedwith AscI and inserted in the single AscI site of the pENTR-DRD1 plasmid(Law et al, 2010), located 6 base pairs after the end of the codingsequence of DRD1.

DMS3-Flag-ZF: The Flag-ZF108-BLRP fusion in the pCR2 plasmid wasdigested with AscI and inserted in the single AscI site of thepENTR-DMS3 plasmid (Law et al, 2010), located 6 base pairs after the endof the coding sequence of DMS3.

RDM1-Flag-ZF: For this purpose, the plasmid pENTR-RDM1 was created,which contains a genomic sequence of RDM1 including 350 base pairs of 5′promoter sequence. The Flag-ZF108-BLRP fusion in the pCR2 plasmid wasthen digested with AscI and inserted in the single AscI site of apENTR-RDM1 plasmid, located 6 base pairs after the end of the codingsequence of RDM1.

RDM1-HA-ZF: For this purpose, the plasmid pENTR-RDM1 was created, whichcontains a genomic sequence of RDM1 including 350 base pairs of 5′promoter sequence. The HA-ZF108-BLRP fusion in the pCR2 plasmid was thendigested with AscI and inserted in the single AscI site of a pENTR-RDM1plasmid, located 6 base pairs after the end of the coding sequence ofRDM1.

HA-ZF-DRM3: For this purpose, the plasmid pENTR-BLRP-HA-DRM3 was used,which contains a genomic sequence of DRM3 including 2500 base pairs of5′ promoter sequence and a BLRP-HA fusion right before the start codon.The ZF108 fragment in the pUC57 plasmid was then digested with XhoI andinserted in the single XhoI site of the pENTR-BLRP-HA-DRM3 plasmid,located between the BLRP and HA tag.

HA-2XZF-DRM3: For this purpose, the plasmid pENTR-BLRP-HA-DRM3 was used,which contains a genomic sequence of DRM3 including 2500 base pairs of5′ promoter sequence and a BLRP-HA fusion right before the start codon.The ZF108 fragment in the pUC57 plasmid was then digested with XhoI andtwo copies of ZF108 were inserted in tandem in the single XhoI site ofthe pENTR-BLRP-HA-DRM3 plasmid, located between the BLRP and HA tag.

ZF-3F9M-DRM2: A ZF108 fragment flanked by EcoRI sites in a pUC57 wasdigested with EcoRI and inserted in the single EcoRI site in the plasmidpENTR-3F9M-DRM2 (Henderson et al., 2010), located at the 5′ start of the3×Flag-9×Myc tag.

FRG-Flag-ZF: For this purpose, the plasmid pENTR-FRG was used thatcontains a genomic sequence of FRG including 800 base pairs of 5′promoter sequence. The Flag-ZF108-BLRP fusion in the pCR2 plasmid wasdigested with AscI and inserted in the single AscI site of the pENTR-FRGplasmid, located 6 base pairs after the end of the coding sequence ofFRG.

SUVR2-Flag-ZF: The plasmid pENTR-SUVR2 was used that contains a genomicsequence of SUVR2 including 2000 base pairs of 5′ promoter sequence. TheFlag-ZF108-BLRP fusion in the pCR2 plasmid was digested with AscI andinserted in the single AscI site of a pENTR-SUVR2 plasmid, located 6base pairs after the end of the coding sequence of SUVR2.

SUVR2-HA-ZF: The plasmid pENTR-SUVR2 was used, that contains a genomicsequence of SUVR2 including 2000 base pairs of 5′ promoter sequence. TheHA-ZF108-BLRP fusion in the pCR2 plasmid was digested with AscI andinserted in the single AscI site of a pENTR-SUVR2 plasmid, located 6base pairs after the end of the coding sequence of SUVR2.

MORC6-HA-ZF: The plasmid pENTR-MORC6 was uded, that contains a genomicsequence of MORC6 including 2463 base pairs of 5′ promoter sequence. TheHA-ZF108-BLRP fusion in the pCR2 plasmid was digested with AscI andinserted in the single AscI site of a pENTR-MORC6 plasmid, located 6base pairs after the end of the coding sequence of MORC6.

Flag-ZF-CMT2: The plasmid pENTR-Flag-CMT2 was generated, which containsa genomic sequence of CMT2 including 1032 base pairs of 5′ promotersequence and a BLRP-Flag fusion right before the start codon. The ZF108fragment in the pUC57 plasmid was digested with XhoI and inserted in thesingle XhoI site of the pENTR-BLRP-Flag-CMT2 plasmid, located betweenthe BLRP and Flag tag.

Introduction of Fusion Proteins into fwa-4

All ZN-108 fusion protein constructs described above were recombinedinto the vector JP726 and introduced into fwa-4 usingagrobacterium-mediated transformation. Transformed lines were selectedfor with BASTA.

Results

To explore whether various other RdDM proteins have the ability totrigger de novo DNA methylation at the FWA locus in the fiva-4 mutant, aseries of experiments were conducted in an attempt to target differentcomponents of the RdDM pathway to the promoter of the TWA gene inArabidopsis. Various proteins involved in RdDM were selected and werefused to the ZF108 zinc finger, which targets the FWA promoter (seeExample 2), and transformed into the fwa-4 mutant. ZF-targeting lineswere constructed as described above, in a fashion analogous to thosedescribed in Examples 2 and 4. The flowering time of −30 independenttransgenic lines was scored. The list of the different RdDM componentschosen and the flowering time results are shown below in Table 13.

TABLE 13 Early flowering in T1 lines compared to fwa-4 Early floweringin T1 Plant Line lines compared to fwa-4 DRD1-IIA-ZF 0% DMS3-Flag-ZF80%  RDM1-Flag-ZF 0% RDM1-HA-ZF 0% HA-2XZF-DRM3 0% HA-ZF-DRM3 0%ZF-3F9M-DRM2 0% FRG-Flag-ZF 0% SUVR2-Flag-ZF 10%  SUVR2-HA-ZF 0%MORC6-HA-ZF 50%  Flag-ZF-CMT2 0%

The results presented in Table 13 demonstrate that DMS3-ZF and MORC6-ZFcan efficiently promote early flowering in an fwa-4 mutant background.SUVR2-Flag-ZF targeting produced 3 out of 30 early flowering plants, butthese plants had not flowered as early as the plants targeted by DMS3 orMORC6. Also, SUVR2-HA-ZF produced no early flowering plants. The SUVR2results suggest that SUVR2 has at least a partial ability, when fused toan FWA-targeting DNA-binding domain, to target and silence FWA.Importantly, of the three proteins in the DDR complex (DRD1, DMS3 andRDM1), only DMS3 was effective at efficiently inducing early floweringrelative to fwa-4 in these first generation T1 plants. Also, directtargeting of DRM2 was not effective. Thus, the results suggest that notall RdDM components are effective in efficiently targeting DNAmethylation, at least in first generation T1 plants.

As can also be seen in Table 13, MORC6-HA-ZF was effective at inducingearly flowering in the fwa-4 mutant. MORC1 (At4g36290) and MORC2(AT4G36280) are proteins related to MORC6 and Applicants have shown thatthey form stable heterodimers with MORC6. MORC6 are MORC1 werepreviously shown by the applicants to be involved in gene silencing(Moissiard et al., 2012). Applicants have also shown that a MORC1 MORC2double mutant has a very similar phenotype as MORC6 mutants. Thus, it isthought that MORC1 and MORC1b are very likely to also successfullytarget Pol V, DNA methylation, and gene silencing.

In order to analyze whether the early flowering phenotype of theearly-flowering lines described in Table 13 was due to the methylationof the FWA promoter, a whole-genome bisulfite sequencing assay wasperformed in two independent DMS3-ZF lines and 3 independent MORC6-ZFlines that showed the early flowering phenotype relative to fwa-4.Bisulfite sequencing experiments were conducted in a fashion analogousto the method described in Example 4. The results showed that DNAmethylation was re-established at FWA in a manner very similar that thatpreviously shown for SUVH2 in Example 4 (FIG. 17). Thus, DMS3 and MORC6were effective in targeting methylation at the FWA promoter. Asdescribed above, the ZF-SUVR2 lines were somewhat effective at inducingearly flowering in fwa-4 mutants, and thus are also likely to target DNAmethylation to FWA.

In order to further analyze the stability of FWA silencing in thesetransgenic plants, and to test whether some fusion proteins might showan effect only in later generations, a number of T1 plants for each linewere allowed to self-pollinate and flowering time was assayed in the T2generation, as shown in Table 14. T2 plants derived from early floweringT1 plants from the DMS3-ZF transformants showed 100% early floweringplants in the T2 generation, demonstrating the effectiveness andstability of TWA gene silencing. T2 plants derived from early floweringT1 plants from the MORC6-ZF transformants showed some variability butstill most showed 100% early flowering plants in the T2 generation. T2plants derived from early flowering T1 plants from the SUVR2-ZFtransformants showed more variability and only one showed 100% earlyflowering plants in the T2 generation.

TABLE 14 Early Flowering in T2 lines Line Early Late % Early floweringwild type Col0 28 0 100%  fwa-4 0 24 0% DRD1-HA ZF 35 1 15 6% 34 1 12 8%23 0 10 0% 32 0 10 0% 31 0 10 0% 30 0 9 0% 29 0 10 0% DMS3-Flag-ZF 7 170 100%  2 14 0 100%  11 8 0 100%  12 7 0 100%  10 10 0 100%  41 8 0100%  9 8 0 100%  RDM1-HA-ZF 15 2 16 11%  6 2 13 13%  14 0 10 0% 16 9 190%  19 6 4 60%  25 1 9 10%  24 0 4 0% RDM1-Flag-ZF 1 0 18 0% 4 0 15 0%10 0 10 0% 9 0 10 0% 8 0 9 0% 2 0 10 0% 5 0 10 0% HA-2XZF-DRM3 32 1 156% 26 0 15 0% 27 18 0 100%  15 0 15 0% 29 1 7 13%  30 0 8 0% 24 0 8 0%28 8 2 80%  31 0 10 0% 25 0 6 0% HA-ZF-DRM3 23 0 18 0% 4 0 14 0% 26 0 50% 3 0 5 0% 27 0 5 0% 25 0 5 0% 24 0 5 0% 22 0 3 0% ZF-3F9M-DRM2 5 17 0100%  6 12 0 100%  18 0 8 0% 19 0 10 0% 20 3 0 100%  21 0 10 0% 13 0 100% FRG-Flag-ZF 32 7 10 41%  4 0 13 0% 14 2 7 22%  16 0 10 0% 19 1 8 11% 27 0 10 0% 2 2 7 22%  1 0 10 0% SUVR2-Flag-ZF 2 15 0 100%  22 8 7 53%  70 10 0% 28 0 9 0% 1 2 7 22%  3 0 8 0% 29 1 8 11%  30 5 3 63%  27 0 10 0%26 1 9 10%  SUVR2-HA-ZF 18 0 18 0% 23 4 10 29%  14 0 10 0% 12 2 7 22%  14 5 44%  2 1 5 17%  3 0 10 0% MORC6-HA-ZF 3 16 1 94%  1 18 0 100%  7 7 0100%  8 7 0 100%  2 10 0 100%  4 4 0 100%  3 9 0 100%  Flag-ZF-CMT2 13 018 0% 7 0 14 0% 14 0 10 0% 1 0 10 0% 22 0 10 0% 23 0 10 0% 24 0 10 0%

Analysis of the T2 generation for other fusion proteins showed that evenfor some RdDM factors that showed no effect in the T1 generation, apartial effect could be seen in the T2 generation. This was found forthe DRD1-ZF, RDM1-ZF, DRM3-ZF, DRM2-ZF, and FRG-ZF (FRG is the geneAt3g20010 which Applicants have shown is involved in RdDM) fusionconstructs. This demonstrates that the DRD1, RDM1, DRM3, DRM2, and FRGgenes may also be useful for targeting Pol V, DNA methylation, and genesilencing, although the efficiency of these genes may be lower and itmay require multiple plant generations to observe an effect. As acontrol, the CMT2 protein was included that is not involved in RdDM, andit was observed that all T2 plants showed 100% late flowering, showingthat CMT2 is not effective in targeting silencing of FWA.

Applicants have shown that different RdDM proteins can be targeted tosilence specific loci with varying degrees of silencing efficiency.There may be some advantage to having a set of proteins that can providea range of different efficiencies of gene silencing. For example,depending on the target nucleic acid to be silenced, it may beadvantageous to select recombinant proteins of the present disclosurehaving different silencing efficiencies. For example, it may be anadvantage to fully silence the expression of a target gene by selectinga very efficient RdDM component to direct as much methylation aspossible to the target gene. In other cases, it might be an advantage totarget a less efficient RdDM component to target less methylation to agene to cause only a partial silencing effect. Genes often showdifferent effects on plant phenotype when they are expressed atdifferent levels, and there are likely to be situations where partialsilencing of a plant gene is most advantageous.

Example 6

The following Example relates to the production and characterization ofa modified A. thaliana SHH1 protein that is engineered to contain anucleic acid binding domain to target the modified SHH1 protein to aspecific nucleic acid sequence, and to the production andcharacterization of a modified A. thaliana SUVH2 protein that isengineered to contain a nucleic acid binding domain to target themodified SUVH2 protein to a specific nucleic acid sequence.

In this Example, the targeting of SHH1 and SUVH2 simultaneously to theSUPERMAN promoter region was associated with the enrichment of DNAmethylation at SUPERMAN.

Materials and Methods

Construction of TAL-SHH1 and TAL-SUVH2 Chimaera

The Gateway entry clone containing SUVH2 including 1.4 kb of thepromoter region and the ORF with N-terminal 3×HA and BLRP tags wasdescribed previously (Johnson et al., 2008). The Gateway entry clonecontaining SHH1 including 1.4 kb of the promoter region and the ORF withC-terminal BLRP and 3×Myc tags was described previously (Law et al.,2011). BsaI recognition sites were removed from the SUVH2 entry clone bysite directed mutagenesis (Quickchange multi, Agilent) using primersSUVH2deltaBsaI1, 5′-TCGTTGTCTCGCCGAAATTCGAAAGACCGAGAGAG-3′ (SEQ ID NO:168), SUVH2deltaBsaI2, 5′-TCATCATAGTGTTGTTATATCTTTGGTGTCTCTGTCTTGCTTC-3′(SEQ ID NO: 175) and SUVH2deltaBsaI3,5′-CCTTTAATTTCCTTTTTTGTTTGCGTCTCTACTCTCTACAATCTATA-3′ (SEQ ID NO: 169).BsaI recognition sites were removed from the SHH1 entry clone by sitedirected mutagenesis (Quickchange II, Agilent) using primersSHH1deltaBsaI_fo, 5′-GGGAGAGTGAACGTTGGTGACCTGCTTCTATGTTT-3′ (SEQ ID NO:170), SHH1deltaBsaLre, 5′-AAACATAGAAGCAGGTCACCAACGTTCACTCTCCC-3′ (SEQ IDNO: 171). After removing the BsaI sites the entry clones were linearizedby restriction digestions with XhoI. In order to insert the DNA sequenceencoding a modified Hax3-based transcription activator-like effector(TALE) (Sanjana et al., 2012) excluding the C-terminal nuclearlocalization signal and acidic activation domain flanked by GSSGSSlinkers in frame in between the C-terminal BLRP and 3×Myc tags of SHH1or the N-terminal 3×HA and BLRP tags of SUVH2, 2.8 kb of the TALEbackbone including the ccdB selection cassette were amplified from TALEtranscriptional activator (TALE-TF) plasmids (Addgene) using primersTALETFintotag_fo,5′-CCAAGGACCTCTCGAGGGATCTTCAGGTTCATCTTCGCGGACCCGGCTCCCT-3′ (SEQ ID NO:144) and TALETFintoSHH1Myc_re,5′-CATAGATCCCTCGAGTGAAGAACCAGATGATCCGCTAGCTGACGCGCGA-3′ (SEQ ID NO: 145)or TALETFintoSUVH2tag_re, 5′-GGTATCCCATCTCGAGTGAAGAACCAGATGATCCGCTAGCTGACGCGCGA-3′ (SEQ ID NO: 172),respectively. Amplicons were fused with the linearized entry clonesusing In-Fusion HD cloning system (Clontech). Two TALE DNA-bindingdomains targeting the sequences 5′-GGGGATTTGATAATGCGTC-3′ (SEQ ID NO:173) (SUP_D) corresponding to chromosome 3 from nucleotide positions8242204 to 8242222 and 5′-GTTAAGACTGTGAAAGAGA-3′ (SEQ ID NO: 174)(SUP_P) corresponding to chromosome 3 from nucleotide positions 8242251to 8242233 in the promoter region of SUPERMAN (AT3G23130) were assembledfrom 18 monomer-repeats (Addgene) by Golden Gate cloning and insertedbetween the BsaI sites flanking the ccdB selection cassette (Sanjana etal., 2012). DNA sequences encoding the TALE target repeats correspondingto SUP_D (SEQ ID NO: 138) and SUP_P (SEQ ID NO: 139) are listed. Inorder to facilitate binding of the TALE fusion proteins to methylatedcytosine the repeat variable “diresidue” (RVD) N* was used (Valton etal., 2012). Plasmids encoding monomer RVDs N* and NH were generated bysite-directed mutagenesis (Quickchange II, Agilent) of the TALE monomertemplate plasmid pNN_v2 (Addgene) using primers NN>N*Jo,5′-GTGGCAATTGCGAGCAACGGGGGAAAGCAG-3′ (SEQ ID NO: 147), NN>N*_re,5′-CTGCTTTCCCCCGTTGCTCGCAATTGCCAC-3′ (SEQ ID NO: 148), NN>NH_fo,5′-GGCAATTGCGAGCAACCATGGGGGAAAGCAGGCAC-3′ (SEQ ID NO: 149) and NN>NH_re,5′-GTGCCTGCTTTCCCCCATGGTTGCTCGCAATTGCC-3′ (SEQ ID NO: 150),respectively. TALE-TF plasmid encoding RVD N* was generated bysite-directed mutagenesis (Quickchange II, Agilent) of pTALE-TF_v2 (NN)(Addgene) using primers TALETF_NN>N*_fo,5′-TGGCTATTGCATCCAACGGGGGCAGACC-3′ (SEQ ID NO: 151) and TALETF_NN>N*_re,5′-GGTCTGCCCCCGTTGGATGCAATAGCCA-3′ (SEQ ID NO: 152). Binary vectors weregenerated using LR clonase II (Life Technologies) and modifiedpEarlyGate302 destination vectors containing Bar or hph selectionmarkers (Law et al., 2011).

Plant Material

TAL-SHH1 constructs were transformed into shhl (SALK_074540), andTAL-SUVH2 into suvh2 (SALK_079574) of ecotype Col-0 by Agrobacteriumtumefaciens strain ABLO using the floral dip method (Clough and Bent,1998). T1 plants were selected with Glufosinate or Hygromycin B andexpression of the chimeric TAL-SHH1 or TAL-SUVH2 proteins was tested byprotein isolation and Western blot with antibodies against the 3×Myc or3×HA tag, respectively. T1 plants showing strong transgene expressionwere crossed in order to combine TAL-SUVH2 with TAL-SHH1 or hairpinconstructs for the target region of the SUPERMAN (At3g23130) gene. F1plants were genotyped by PCR to determine the presence of thetransgenes.

Results

After selecting F1 plants containing either the TAL-SHH1 directedagainst the SUPERMAN gene, a TAL-SUVH2 directed against the SUPERMANgene, or a plant containing both the TAL-SHH1 and TAL-SUVH2 transgenes,whole genome bisulfite libraries were prepared using establishedprotocols (Law et al., 2013). These libraries were deeply sequenced andreads were mapped to the Arabidopsis genome as previously described (Lawet al., 2013). As shown in FIG. 19, CHH DNA methylation was detected atthe SUPERMAN gene in plants containing both the TAL-SHH1 and TAL-SUVH2transgenes, but not in plants containing either the TAL-SHH1 orTAL-SUVH2 transgenes alone. These results suggest that targeting SHH1and SUVH2 to the SUPERMAN promoter region was sufficient to cause CHHDNA methylation.

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STATEMENTS OF EMBODIMENTS

-   1. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising        an SHH1 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   2. The method of embodiment 1, wherein the DNA-binding domain    comprises a zinc finger domain.-   3. The method of embodiment 2, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   4. The method of embodiment 2, wherein the zinc finger domain is a    zinc finger array.-   5. The method of embodiment 2, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   6. The method of embodiment 1, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   7. The method of embodiment 1, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   8. The method of embodiment 1, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   9. The method of any one of embodiments 1-8, wherein the second    amino acid sequence comprises at least one of a homeodomain or a    SAWADEE domain.-   10. The method of embodiment 1, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 1.-   11. The method of embodiment 1, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 1.-   12. The method of any one of embodiments 1-11, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   13. The method of embodiment 12, wherein the RNA polymerase is RNA    polymerase IV.-   14. The method of any one of embodiments 1-13, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   15. The method of any one of embodiments 1-14, wherein the one or    more target nucleic acids are endogenous nucleic acids.-   16. The method of any one of embodiments 1-14, wherein the one or    more target nucleic acids are heterologous nucleic acids.-   17. The method of any one of embodiments 1-16, wherein expression of    the one or more target nucleic acids is silenced.-   18. A recombinant nucleic acid encoding an SHH1-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising an SHH1    polypeptide or a fragment thereof.-   19. The recombinant nucleic acid of embodiment 18, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 1.-   20. The recombinant nucleic acid of embodiment 18, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 1.-   21. The recombinant nucleic acid of any one of embodiments 18-20,    wherein the DNA-binding domain comprises a zinc finger domain.-   22. The recombinant nucleic acid of embodiment 21, wherein the zinc    finger domain comprises two, three, four, five, six, seven, eight,    or nine zinc fingers.-   23. The recombinant nucleic acid of embodiment 21, wherein the zinc    finger domain is a zinc finger array.-   24. The recombinant nucleic acid of embodiment 21, wherein the zinc    finger domain is selected from the group consisting of a C2H2 zinc    finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   25. The recombinant nucleic acid of any one of embodiments 18-20,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   26. The recombinant nucleic acid of any one of embodiments 18-20,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   27. The recombinant nucleic acid of any one of embodiments 18-20,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   28. The recombinant nucleic acid of embodiment 27, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   29. The recombinant nucleic acid of embodiment 27, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   30. The recombinant nucleic acid of embodiment 27, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   31. The recombinant nucleic acid of any one of embodiments 27-30,    wherein the SHH1-like protein reduces expression of the one or more    target nucleic acids.-   32. The recombinant nucleic acid of any one of embodiments 27-30,    wherein the SHH1-like protein silences expression of the one or more    target nucleic acids.-   33. A vector comprising the recombinant nucleic acid of any one of    embodiments 18-32, wherein the recombinant nucleic acid is operably    linked to a regulatory sequence.-   34. A host cell comprising the expression vector of embodiment 33.-   35. The host cell of embodiment 34, wherein the host cell is a plant    cell.-   36. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 18-32.-   37. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising a        SUVH2 polypeptide or a fragment thereof, or a SUVH9 polypeptide        or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   38. The method of embodiment 37, wherein the DNA-binding domain    comprises a zinc finger domain.-   39. The method of embodiment 38, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   40. The method of embodiment 38, wherein the zinc finger domain is a    zinc finger array.-   41. The method of embodiment 38, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   42. The method of embodiment 37, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   43. The method of embodiment 37, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   44. The method of embodiment 37, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   45. The method of any one of embodiments 37-45, wherein the second    amino acid sequence comprises a domain selected from the group    consisting of a two-helix bundle domain, a SRA domain, a pre-SET    domain, and a SET domain.-   46. The method of embodiment 37, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 14    or SEQ ID NO: 27.-   47. The method of embodiment 37, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 14 or SEQ ID NO: 27.-   48. The method of any one of embodiments 37-47, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   49. The method of embodiment 48, wherein the RNA polymerase is RNA    polymerase V.-   50. The method of any one of embodiments 37-49, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   51. The method of any one of embodiment 37-50, wherein the one or    more target nucleic acids are endogenous nucleic acids.-   52. The method of any one of embodiments 37-50, wherein the one or    more target nucleic acids are heterologous nucleic acids.-   53. The method of any one of embodiments 37-52, wherein expression    of the one or more target nucleic acids is silenced.-   54. A recombinant nucleic acid encoding a SUVH2-like protein or a    SUVH9-like protein comprising a first amino acid sequence comprising    a DNA-binding domain and a second amino acid sequence comprising a    SUVH2 polypeptide or a fragment thereof, or a SUVH9 polypeptide or a    fragment thereof.-   55. The recombinant nucleic acid of embodiment 54, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75% at least 80%, at least 85%, at least 90%, at least    91%, at least 92%, at least 93%, at least 94%, at least 95%, at    least 96%, at least 97%, at least 98%, or at least 99% identical to    SEQ ID NO: 14 or SEQ ID NO: 27.-   56. The recombinant nucleic acid of embodiment 54, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 14 or SEQ ID NO: 27.-   57. The recombinant nucleic acid of any one of embodiments 54-56,    wherein the DNA-binding domain comprises a zinc finger domain.-   58. The recombinant nucleic acid of embodiment 57, wherein the zinc    finger domain comprises two, three, four, five, six, seven, eight,    or nine zinc fingers.-   59. The recombinant nucleic acid of embodiment 57, wherein the zinc    finger domain is a zinc finger array.-   60. The recombinant nucleic acid of embodiment 57, wherein the zinc    finger domain is selected from the group consisting of a C2H2 zinc    finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   61. The recombinant nucleic acid of any one of embodiments 54-56,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   62. The recombinant nucleic acid of any one of embodiments 54-56,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   63. The recombinant nucleic acid of any one of embodiments 54-62,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   64. The recombinant nucleic acid of embodiment 63, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   65. The recombinant nucleic acid of embodiment 63, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   66. The recombinant nucleic acid of embodiment 63, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   67. The recombinant nucleic acid of any one of embodiments 63-66,    wherein the SUVH2-like protein or SUVH9-like protein reduces    expression of the one or more target nucleic acids.-   68. A vector comprising the recombinant nucleic acid of any one of    embodiments 54-67, wherein the recombinant nucleic acid is operably    linked to a regulatory sequence.-   69. A host cell comprising the expression vector of embodiment 68.-   70. The host cell of embodiment 69, wherein the host cell is a plant    cell.-   71. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 54-67.-   72. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising:        -   a first recombinant nucleic acid encoding a first            recombinant polypeptide comprising a first amino acid            sequence comprising a DNA-binding domain and a second amino            acid sequence comprising an SHH1 polypeptide or a fragment            thereof, and        -   a second recombinant nucleic acid encoding a second            recombinant polypeptide comprising a first amino acid            sequence comprising a DNA-binding domain and a second amino            acid sequence comprising a SUVH2 polypeptide or a fragment            thereof, or a SUVH9 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the first        recombinant polypeptide encoded by the first recombinant nucleic        acid and the second recombinant polypeptide encoded by the        second recombinant nucleic acid are expressed and bind to the        one or more target nucleic acids, thereby reducing expression of        the one or more target nucleic acids.-   73. The method of embodiment 72, wherein at least one of the first    or second recombinant polypeptides induces RNA-directed DNA    methylation.-   74. The method of any one of embodiments 72-73, wherein the one or    more target nucleic acids are endogenous nucleic acids.-   75. The method of any one of embodiments 72-73, wherein the one or    more target nucleic acids are heterologous nucleic acids.-   76. The method of any one of embodiment 72-75, wherein expression of    the one or more target nucleic acids is silenced.-   77. A host cell comprising the expression vectors of embodiments 33    and 68.-   78. The host cell of embodiment 77, wherein the host cell is a plant    cell.-   79. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 18-32 and any one of embodiments 54-67.-   80. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising a        DMS3 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   81. The method of embodiment 80, wherein the DNA-binding domain    comprises a zinc finger domain.-   82. The method of embodiment 81, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   83. The method of embodiment 81, wherein the zinc finger domain is a    zinc finger array.-   84. The method of embodiment 81, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   85. The method of embodiment 80, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   86. The method of embodiment 80, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   87. The method of embodiment 80, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   88. The method of embodiment 80, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 41.-   89. The method of embodiment 80, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 41.-   90. The method of any one of embodiments 80-89, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   91. The method of any one of embodiments 80-90, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   92. The method of any one of embodiments 80-91, wherein the one or    more target nucleic acids are endogenous nucleic acids.-   93. The method of any one of embodiments 80-91, wherein the one or    more target nucleic acids are heterologous nucleic acids.-   94. The method of any one of embodiments 80-93, wherein expression    of the one or more target nucleic acids is silenced.-   95. A recombinant nucleic acid encoding a DMS3-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising a DMS3    polypeptide or a fragment thereof.-   96. The recombinant nucleic acid of embodiment 95, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 41.-   97. The recombinant nucleic acid of embodiment 96, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 41.-   98. The recombinant nucleic acid of any one of embodiments 95-97,    wherein the DNA-binding domain comprises a zinc finger domain.-   99. The recombinant nucleic acid of embodiment 98, wherein the zinc    finger domain comprises two, three, four, five, six, seven, eight,    or nine zinc fingers.

100. The recombinant nucleic acid of embodiment 98, wherein the zincfinger domain is a zinc finger array.

101. The recombinant nucleic acid of embodiment 98, wherein the zincfinger domain is selected from the group consisting of a C2H2 zincfinger domain, a CCCH zinc finger domain, a multi-cysteine zinc fingerdomain, and a zinc binuclear cluster domain.

102. The recombinant nucleic acid of any one of embodiments 95-97,wherein the DNA-binding domain is selected from the group consisting ofa TAL effector targeting domain, a helix-turn-helix family DNA-bindingdomain, a basic domain, a ribbon-helix-helix domain, a TBP domain, abarrel dimer domain, a real homology domain, a BAH domain, a SANTdomain, a Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, aWD40 domain, and a MBD domain.

-   103. The recombinant nucleic acid of any one of embodiments 95-97,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.

104. The recombinant nucleic acid of any one of embodiments 95-97,wherein the DNA-binding domain binds one or more target nucleic acids.

105. The recombinant nucleic acid of embodiment 104, wherein the one ormore target nucleic acids are polypeptide-encoding nucleic acids.

106. The recombinant nucleic acid of embodiment 104, wherein the one ormore target nucleic acids are endogenous plant nucleic acids.

107. The recombinant nucleic acid of embodiment 104, wherein the one ormore target nucleic acids are heterologous nucleic acids.

108. The recombinant nucleic acid of any one of embodiments 104-107,wherein the DMS3-like protein reduces expression of the one or moretarget nucleic acids.

109. The recombinant nucleic acid of any one of embodiments 104-107,wherein the DMS3-like protein silences expression of the one or moretarget nucleic acids.

110. A vector comprising the recombinant nucleic acid of any one ofembodiments 95-109, wherein the recombinant nucleic acid is operablylinked to a regulatory sequence.

111. A host cell comprising the expression vector of embodiment 110.

-   112. The host cell of embodiment 111, wherein the host cell is a    plant cell.-   113. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 95-112.-   114. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising a        MORC6 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   115. The method of embodiment 114, wherein the DNA-binding domain    comprises a zinc finger domain.-   116. The method of embodiment 115, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   117. The method of embodiment 115, wherein the zinc finger domain is    a zinc finger array.-   118. The method of embodiment 115, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   119. The method of embodiment 114, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   120. The method of embodiment 114, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   121. The method of embodiment 114, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   122. The method of embodiment 114, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 53.-   123. The method of embodiment 114, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 53.-   124. The method of any one of embodiments 114-123, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   125. The method of any one of embodiments 114-123, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   126. The method of any one of embodiments 114-125, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   127. The method of any one of embodiments 114-125, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   128. The method of any one of embodiments 114-127, wherein    expression of the one or more target nucleic acids is silenced.-   129. A recombinant nucleic acid encoding a MORC6-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising a MORC6    polypeptide or a fragment thereof.-   130. The recombinant nucleic acid of embodiment 129, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 53.-   131. The recombinant nucleic acid of embodiment 130, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 53.-   132. The recombinant nucleic acid of any one of embodiments 129-131,    wherein the DNA-binding domain comprises a zinc finger domain.-   133. The recombinant nucleic acid of embodiment 132, wherein the    zinc finger domain comprises two, three, four, five, six, seven,    eight, or nine zinc fingers.-   134. The recombinant nucleic acid of embodiment 132, wherein the    zinc finger domain is a zinc finger array.-   135. The recombinant nucleic acid of embodiment 132, wherein the    zinc finger domain is selected from the group consisting of a C2H2    zinc finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   136. The recombinant nucleic acid of any one of embodiments 129-131,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   137. The recombinant nucleic acid of any one of embodiments 129-131,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   138. The recombinant nucleic acid of any one of embodiments 129-131,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   139. The recombinant nucleic acid of embodiment 138, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   140. The recombinant nucleic acid of embodiment 138, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   141. The recombinant nucleic acid of embodiment 138, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   142. The recombinant nucleic acid of any one of embodiments 138-141,    wherein the MORC6-like protein reduces expression of the one or more    target nucleic acids.-   143. The recombinant nucleic acid of any one of embodiments 138-141,    wherein the MORC6-like protein silences expression of the one or    more target nucleic acids.-   144. A vector comprising the recombinant nucleic acid of any one of    embodiments 114-143, wherein the recombinant nucleic acid is    operably linked to a regulatory sequence.-   145. A host cell comprising the expression vector of    embodiment 144. 146. The host cell of embodiment 145, wherein the    host cell is a plant cell.-   147. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 114-143.-   148. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising a        SUVR2 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   149. The method of embodiment 148, wherein the DNA-binding domain    comprises a zinc finger domain.-   150. The method of embodiment 149, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   151. The method of embodiment 149, wherein the zinc finger domain is    a zinc finger array.-   152. The method of embodiment 149, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   153. The method of embodiment 148, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   154. The method of embodiment 148, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   155. The method of embodiment 148, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   156. The method of embodiment 148, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 66.-   157. The method of embodiment 148, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 66.-   158. The method of any one of embodiments 148-157, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   159. The method of any one of embodiments 148-157, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   160. The method of any one of embodiments 148-159, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   161. The method of any one of embodiments 148-159, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   162. The method of any one of embodiments 148-161, wherein    expression of the one or more target nucleic acids is silenced.-   163. A recombinant nucleic acid encoding a SUVR2-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising a SUVR2    polypeptide or a fragment thereof.-   164. The recombinant nucleic acid of embodiment 163, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 66.-   165. The recombinant nucleic acid of embodiment 164, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 66.-   166. The recombinant nucleic acid of any one of embodiments 163-165,    wherein the DNA-binding domain comprises a zinc finger domain.-   167. The recombinant nucleic acid of embodiment 166, wherein the    zinc finger domain comprises two, three, four, five, six, seven,    eight, or nine zinc fingers.-   168. The recombinant nucleic acid of embodiment 166, wherein the    zinc finger domain is a zinc finger array.-   169. The recombinant nucleic acid of embodiment 166, wherein the    zinc finger domain is selected from the group consisting of a C2H2    zinc finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   170. The recombinant nucleic acid of any one of embodiments 163-165,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   171. The recombinant nucleic acid of any one of embodiments 163-165,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   172. The recombinant nucleic acid of any one of embodiments 163-165,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   173. The recombinant nucleic acid of embodiment 172, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   174. The recombinant nucleic acid of embodiment 172, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   175. The recombinant nucleic acid of embodiment 172, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   176. The recombinant nucleic acid of any one of embodiments 172-175,    wherein the SUVR2-like protein reduces expression of the one or more    target nucleic acids.-   177. The recombinant nucleic acid of any one of embodiments 172-175,    wherein the SUVR2-like protein silences expression of the one or    more target nucleic acids.-   178. A vector comprising the recombinant nucleic acid of any one of    embodiments 163-177, wherein the recombinant nucleic acid is    operably linked to a regulatory sequence.-   179. A host cell comprising the expression vector of embodiment 178.-   180. The host cell of embodiment 179, wherein the host cell is a    plant cell.-   181. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 163-177.-   182. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising:        -   a first recombinant nucleic acid encoding a first            recombinant polypeptide comprising a first amino acid            sequence comprising a DNA-binding domain and a second amino            acid sequence comprising an SHH1 polypeptide or a fragment            thereof, and        -   one or more additional recombinant nucleic acids encoding            one or more additional polypeptides, each of the one or more            additional polypeptides comprising a first amino acid            sequence comprising a DNA-binding domain and a second amino            acid sequence comprising a polypeptide selected from the            group consisting of a SUVH2 polypeptide or a fragment            thereof, a SUVH9 polypeptide or a fragment thereof, a DMS3            polypeptide or a fragment thereof, a MORC6 polypeptide or a            fragment thereof, and a SUVR2 polypeptide or a fragment            thereof; and    -   (b) growing the plant under conditions whereby the first        recombinant polypeptide encoded by the first recombinant nucleic        acid and the one or more additional polypeptides encoded by the        one or more additional recombinant nucleic acids are expressed        and bind to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   183. The method of embodiment 182, wherein at least one of the    recombinant polypeptides induces RNA-directed DNA methylation.-   184. The method of any one of embodiments 182-183, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   185. The method of any one of embodiments 182-183, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   186. The method of any one of embodiments 182-185, wherein    expression of the one or more target nucleic acids is silenced.-   187. A host cell comprising expression vectors comprising the    recombinant nucleic acids encoding the recombinant polypeptides of    embodiment 182.

188. The host cell of embodiment 187, wherein the host cell is a plantcell.

-   189. A recombinant plant comprising the recombinant nucleic acids of    embodiment 182.-   190. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising a        DRD1 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   191. The method of embodiment 190, wherein the DNA-binding domain    comprises a zinc finger domain.-   192. The method of embodiment 191, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   193. The method of embodiment 191, wherein the zinc finger domain is    a zinc finger array.-   194. The method of embodiment 191, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   195. The method of embodiment 190, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   196. The method of embodiment 190, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   197. The method of embodiment 190, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   198. The method of embodiment 190, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 79.-   199. The method of embodiment 100, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 79.-   200. The method of any one of embodiments 190-199, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   201. The method of any one of embodiments 190-199, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   202. The method of any one of embodiments 190-201, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   203. The method of any one of embodiments 190-201, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   204. The method of any one of embodiments 190-203, wherein    expression of the one or more target nucleic acids is silenced.-   205. A recombinant nucleic acid encoding a DRD1-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising a DRD1    polypeptide or a fragment thereof.-   206. The recombinant nucleic acid of embodiment 205, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 79.-   207. The recombinant nucleic acid of embodiment 206, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 79.-   208. The recombinant nucleic acid of any one of embodiments 205-207,    wherein the DNA-binding domain comprises a zinc finger domain.-   209. The recombinant nucleic acid of embodiment 208, wherein the    zinc finger domain comprises two, three, four, five, six, seven,    eight, or nine zinc fingers.-   210. The recombinant nucleic acid of embodiment 208, wherein the    zinc finger domain is a zinc finger array.-   211. The recombinant nucleic acid of embodiment 208, wherein the    zinc finger domain is selected from the group consisting of a C2H2    zinc finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   212. The recombinant nucleic acid of any one of embodiments 205-207,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   213. The recombinant nucleic acid of any one of embodiments 205-207,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   214. The recombinant nucleic acid of any one of embodiments 205-207,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   215. The recombinant nucleic acid of embodiment 214, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   216. The recombinant nucleic acid of embodiment 214, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   217. The recombinant nucleic acid of embodiment 214, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   218. The recombinant nucleic acid of any one of embodiments 214-217,    wherein the DRD1-like protein reduces expression of the one or more    target nucleic acids.-   219. The recombinant nucleic acid of any one of embodiments 214-217,    wherein the DRD1-like protein silences expression of the one or more    target nucleic acids.-   220. A vector comprising the recombinant nucleic acid of any one of    embodiments 205-219, wherein the recombinant nucleic acid is    operably linked to a regulatory sequence.-   221. A host cell comprising the expression vector of embodiment 220.-   222. The host cell of embodiment 221, wherein the host cell is a    plant cell.-   223. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 205-219.-   224. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising        an RDM1 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   225. The method of embodiment 224, wherein the DNA-binding domain    comprises a zinc finger domain.-   226. The method of embodiment 225, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   227. The method of embodiment 225, wherein the zinc finger domain is    a zinc finger array.-   228. The method of embodiment 225, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   229. The method of embodiment 224, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   230. The method of embodiment 224, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   231. The method of embodiment 224, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   232. The method of embodiment 224, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 91.-   233. The method of embodiment 232, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 91.-   234. The method of any one of embodiments 224-233, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   235. The method of any one of embodiments 224-233, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   236. The method of any one of embodiments 224-235, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   237. The method of any one of embodiments 224-235, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   238. The method of any one of embodiments 224-237, wherein    expression of the one or more target nucleic acids is silenced.-   239. A recombinant nucleic acid encoding an RDM1-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising an RDM1    polypeptide or a fragment thereof.-   240. The recombinant nucleic acid of embodiment 239, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 91.-   241. The recombinant nucleic acid of embodiment 240, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 91.-   242. The recombinant nucleic acid of any one of embodiments 239-241,    wherein the DNA-binding domain comprises a zinc finger domain.-   243. The recombinant nucleic acid of embodiment 242, wherein the    zinc finger domain comprises two, three, four, five, six, seven,    eight, or nine zinc fingers.-   244. The recombinant nucleic acid of embodiment 242, wherein the    zinc finger domain is a zinc finger array.-   245. The recombinant nucleic acid of embodiment 242, wherein the    zinc finger domain is selected from the group consisting of a C2H2    zinc finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   246. The recombinant nucleic acid of any one of embodiments 239-241,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   247. The recombinant nucleic acid of any one of embodiments 239-241,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   248. The recombinant nucleic acid of any one of embodiments 239-241,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   249. The recombinant nucleic acid of embodiment 248, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   250. The recombinant nucleic acid of embodiment 248, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   251. The recombinant nucleic acid of embodiment 248, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   252. The recombinant nucleic acid of any one of embodiments 248-251,    wherein the RDM1-like protein reduces expression of the one or more    target nucleic acids.-   253. The recombinant nucleic acid of any one of embodiments 248-251,    wherein the RDM1-like protein silences expression of the one or more    target nucleic acids.-   254. A vector comprising the recombinant nucleic acid of any one of    embodiments 239-253, wherein the recombinant nucleic acid is    operably linked to a regulatory sequence.-   255. A host cell comprising the expression vector of embodiment 254.-   256. The host cell of embodiment 255, wherein the host cell is a    plant cell.-   257. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 239-253.-   258. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising a        DRM3 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   259. The method of embodiment 258, wherein the DNA-binding domain    comprises a zinc finger domain.-   260. The method of embodiment 259, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   261. The method of embodiment 259, wherein the zinc finger domain is    a zinc finger array.-   262. The method of embodiment 259, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   263. The method of embodiment 258, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   264. The method of embodiment 258, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   265. The method of embodiment 258, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   266. The method of embodiment 258, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO:    101.-   267. The method of embodiment 266, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 101.-   268. The method of any one of embodiments 258-267, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   269. The method of any one of embodiments 258-267, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   270. The method of any one of embodiments 258-269, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   271. The method of any one of embodiments 258-269, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   272. The method of any one of embodiments 258-271, wherein    expression of the one or more target nucleic acids is silenced.-   273. A recombinant nucleic acid encoding a DRM3-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising a DRM3    polypeptide or a fragment thereof.-   274. The recombinant nucleic acid of embodiment 273, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 101.-   275. The recombinant nucleic acid of embodiment 274, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 101.-   276. The recombinant nucleic acid of any one of embodiments 273-275,    wherein the DNA-binding domain comprises a zinc finger domain.-   277. The recombinant nucleic acid of embodiment 276, wherein the    zinc finger domain comprises two, three, four, five, six, seven,    eight, or nine zinc fingers.-   278. The recombinant nucleic acid of embodiment 276, wherein the    zinc finger domain is a zinc finger array.-   279. The recombinant nucleic acid of embodiment 276, wherein the    zinc finger domain is selected from the group consisting of a C2H2    zinc finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   280. The recombinant nucleic acid of any one of embodiments 273-275,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   281. The recombinant nucleic acid of any one of embodiments 273-275,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   282. The recombinant nucleic acid of any one of embodiments 273-275,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   283. The recombinant nucleic acid of embodiment 282, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   284. The recombinant nucleic acid of embodiment 282, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   285. The recombinant nucleic acid of embodiment 282, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   286. The recombinant nucleic acid of any one of embodiments 282-285,    wherein the DRM3-like protein reduces expression of the one or more    target nucleic acids.-   287. The recombinant nucleic acid of any one of embodiments 282-285,    wherein the DRM3-like protein silences expression of the one or more    target nucleic acids.-   288. A vector comprising the recombinant nucleic acid of any one of    embodiments 273-287, wherein the recombinant nucleic acid is    operably linked to a regulatory sequence.-   289. A host cell comprising the expression vector of embodiment 288.-   290. The host cell of embodiment 289, wherein the host cell is a    plant cell.-   291. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 273-287.-   292. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising a        DRM2 polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   293. The method of embodiment 292, wherein the DNA-binding domain    comprises a zinc finger domain.-   294. The method of embodiment 293, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   295. The method of embodiment 293, wherein the zinc finger domain is    a zinc finger array.-   296. The method of embodiment 293, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   297. The method of embodiment 292, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   298. The method of embodiment 292, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   299. The method of embodiment 292, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   300. The method of embodiment 292, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO:    113.-   301. The method of embodiment 300, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 113.-   302. The method of any one of embodiments 292-301, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   303. The method of any one of embodiments 292-301, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   304. The method of any one of embodiments 292-303, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   305. The method of any one of embodiments 292-303, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   306. The method of any one of embodiments 292-305, wherein    expression of the one or more target nucleic acids is silenced.-   307. A recombinant nucleic acid encoding a DRM2-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising a DRM2    polypeptide or a fragment thereof.-   308. The recombinant nucleic acid of embodiment 307, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 113.-   309. The recombinant nucleic acid of embodiment 308, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 113.-   310. The recombinant nucleic acid of any one of embodiments 307-309,    wherein the DNA-binding domain comprises a zinc finger domain.-   311. The recombinant nucleic acid of embodiment 310, wherein the    zinc finger domain comprises two, three, four, five, six, seven,    eight, or nine zinc fingers.-   312. The recombinant nucleic acid of embodiment 310, wherein the    zinc finger domain is a zinc finger array.-   313. The recombinant nucleic acid of embodiment 310, wherein the    zinc finger domain is selected from the group consisting of a C2H2    zinc finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   314. The recombinant nucleic acid of any one of embodiments 307-309,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   315. The recombinant nucleic acid of any one of embodiments 307-309,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   316. The recombinant nucleic acid of any one of embodiments 307-309,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   317. The recombinant nucleic acid of embodiment 316, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   318. The recombinant nucleic acid of embodiment 316, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   319. The recombinant nucleic acid of embodiment 316, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   320. The recombinant nucleic acid of any one of embodiments 316-319,    wherein the DRM2-like protein reduces expression of the one or more    target nucleic acids.-   321. The recombinant nucleic acid of any one of embodiments 316-319,    wherein the DRM2-like protein silences expression of the one or more    target nucleic acids.-   322. A vector comprising the recombinant nucleic acid of any one of    embodiments 307-321, wherein the recombinant nucleic acid is    operably linked to a regulatory sequence.-   323. A host cell comprising the expression vector of embodiment 322.-   324. The host cell of embodiment 323, wherein the host cell is a    plant cell.-   325. A recombinant plant comprising the recombinant nucleic acid of    any one of embodiments 307-321.-   326. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising a recombinant nucleic acid,        wherein the recombinant nucleic acid encodes a recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising        an FRG polypeptide or a fragment thereof; and    -   (b) growing the plant under conditions whereby the recombinant        polypeptide encoded by the recombinant nucleic acid is expressed        and binds to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   327. The method of embodiment 326, wherein the DNA-binding domain    comprises a zinc finger domain.-   328. The method of embodiment 327, wherein the zinc finger domain    comprises two, three, four, five, six, seven, eight, or nine zinc    fingers.-   329. The method of embodiment 327, wherein the zinc finger domain is    a zinc finger array.-   330. The method of embodiment 327, wherein the zinc finger domain is    selected from the group consisting of a Cys2His2 (C2H2) zinc finger    domain, a CCCH zinc finger domain, a multi-cysteine zinc finger    domain, and a zinc binuclear cluster domain.-   331. The method of embodiment 326, wherein the DNA-binding domain is    selected from the group consisting of a TAL effector targeting    domain, a helix-turn-helix family DNA-binding domain, a basic    domain, a ribbon-helix-helix domain, a TBP domain, a barrel dimer    domain, a real homology domain, a BAH domain, a SANT domain, a    Chromodomain, a Tudor domain, a Bromodomain, a PHD domain, a WD40    domain, and a MBD domain.-   332. The method of embodiment 326, wherein the DNA-binding domain    comprises a TAL effector targeting domain.-   333. The method of embodiment 326, wherein the DNA-binding domain    comprises three C2H2 zinc finger domains.-   334. The method of embodiment 326, wherein the second amino acid    sequence comprises an amino acid sequence that is at least 50%, at    least 55%, at least 60%, at least 65%, at least 70%, at least 75%,    at least 80%, at least 85%, at least 90%, at least 91%, at least    92%, at least 93%, at least 94%, at least 95%, at least 96%, at    least 97%, at least 98%, or at least 99% identical to SEQ ID NO:    125.-   335. The method of embodiment 334, wherein the second amino acid    sequence comprises an amino acid sequence that is 100% identical to    SEQ ID NO: 125.-   336. The method of any one of embodiments 326-335, wherein the    recombinant polypeptide interacts with an RNA polymerase.-   337. The method of any one of embodiments 326-335, wherein the    recombinant polypeptide induces RNA-directed DNA methylation.-   338. The method of any one of embodiments 326-337, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   339. The method of any one of embodiments 326-337, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   340. The method of any one of embodiments 326-339, wherein    expression of the one or more target nucleic acids is silenced.-   341. A recombinant nucleic acid encoding an FRG-like protein    comprising a first amino acid sequence comprising a DNA-binding    domain and a second amino acid sequence comprising a FRG polypeptide    or a fragment thereof.-   342. The recombinant nucleic acid of embodiment 341, wherein the    second amino acid sequence comprises an amino acid sequence that is    at least 50%, at least 55%, at least 60%, at least 65%, at least    70%, at least 75%, at least 80%, at least 85%, at least 90%, at    least 91%, at least 92%, at least 93%, at least 94%, at least 95%,    at least 96%, at least 97%, at least 98%, or at least 99% identical    to SEQ ID NO: 125.-   343. The recombinant nucleic acid of embodiment 342, wherein the    second amino acid sequence comprises an amino acid sequence that is    100% identical to SEQ ID NO: 125.-   344. The recombinant nucleic acid of any one of embodiments 341-343,    wherein the DNA-binding domain comprises a zinc finger domain.-   345. The recombinant nucleic acid of embodiment 344, wherein the    zinc finger domain comprises two, three, four, five, six, seven,    eight, or nine zinc fingers.-   346. The recombinant nucleic acid of embodiment 344, wherein the    zinc finger domain is a zinc finger array.-   347. The recombinant nucleic acid of embodiment 344, wherein the    zinc finger domain is selected from the group consisting of a C2H2    zinc finger domain, a CCCH zinc finger domain, a multi-cysteine zinc    finger domain, and a zinc binuclear cluster domain.-   348. The recombinant nucleic acid of any one of embodiments 341-343,    wherein the DNA-binding domain is selected from the group consisting    of a TAL effector targeting domain, a helix-turn-helix family    DNA-binding domain, a basic domain, a ribbon-helix-helix domain, a    TBP domain, a barrel dimer domain, a real homology domain, a BAH    domain, a SANT domain, a Chromodomain, a Tudor domain, a    Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.-   349. The recombinant nucleic acid of any one of embodiments 341-343,    wherein the DNA-binding domain comprises a TAL effector targeting    domain.-   350. The recombinant nucleic acid of any one of embodiments 341-343,    wherein the DNA-binding domain binds one or more target nucleic    acids.-   351. The recombinant nucleic acid of embodiment 350, wherein the one    or more target nucleic acids are polypeptide-encoding nucleic acids.-   352. The recombinant nucleic acid of embodiment 350, wherein the one    or more target nucleic acids are endogenous plant nucleic acids.-   353. The recombinant nucleic acid of embodiment 350, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   354. The recombinant nucleic acid of any one of embodiments 350-353,    wherein the FRG-like protein reduces expression of the one or more    target nucleic acids.-   355. The recombinant nucleic acid of any one of embodiments 350-353,    wherein the FRG-like protein silences expression of the one or more    target nucleic acids.-   356. A vector comprising the recombinant nucleic acid of any one of    embodiments 341-355, wherein the recombinant nucleic acid is    operably linked to a regulatory sequence.-   357. A host cell comprising the expression vector of    embodiment 356. 358. The host cell of embodiment 357, wherein the    host cell is a plant cell. 359. A recombinant plant comprising the    recombinant nucleic acid of any one of embodiments 341-355.-   360. A method for reducing expression of one or more target nucleic    acids in a plant, comprising:    -   (a) providing a plant comprising:    -   a first recombinant nucleic acid encoding a first recombinant        polypeptide comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising        an SHH1 polypeptide or a fragment thereof, and    -   one or more additional recombinant nucleic acids encoding one or        more additional polypeptides, each of the one or more additional        polypeptides comprising a first amino acid sequence comprising a        DNA-binding domain and a second amino acid sequence comprising a        polypeptide selected from the group consisting of a SUVH2        polypeptide or a fragment thereof, a SUVH9 polypeptide or a        fragment thereof, a DMS3 polypeptide or a fragment thereof, a        MORC6 polypeptide or a fragment thereof, a SUVR2 polypeptide or        a fragment thereof, a DRD1 polypeptide or a fragment thereof; an        RDM1 polypeptide or a fragment thereof; a DRM3 polypeptide or a        fragment thereof; a DRM2 polypeptide or a fragment thereof; and        an FRG polypeptide or a fragment thereof, and    -   (b) growing the plant under conditions whereby the first        recombinant polypeptide encoded by the first recombinant nucleic        acid and the one or more additional polypeptides encoded by the        one or more additional recombinant nucleic acids are expressed        and bind to the one or more target nucleic acids, thereby        reducing expression of the one or more target nucleic acids.-   361. The method of embodiment 360, wherein at least one of the    recombinant polypeptides induces RNA-directed DNA methylation.-   362. The method of any one of embodiments 360-361, wherein the one    or more target nucleic acids are endogenous nucleic acids.-   363. The method of any one of embodiments 360-361, wherein the one    or more target nucleic acids are heterologous nucleic acids.-   364. The method of any one of embodiments 360-363, wherein    expression of the one or more target nucleic acids is silenced.-   365. A host cell comprising expression vectors comprising the    recombinant nucleic acids encoding the recombinant polypeptides of    embodiment 360.-   366. The host cell of embodiment 365, wherein the host cell is a    plant cell.-   367. A recombinant plant comprising the recombinant nucleic acids of    embodiment 360.-   368. A plant having reduced expression of one or more target nucleic    acids as a consequence of the method of any one of embodiments 1-17,    37-53, 80-94, 114-128, 148-162, 190-204, 224-238, 258-272, 292-306,    and 326-340.-   369. A progeny plant of the plant of embodiment 368.-   370. The progeny plant of embodiment 369, wherein the progeny plant    has reduced expression of the one or more target nucleic acids and    does not comprise the recombinant nucleic acid.-   371. A plant having reduced expression of one or more target nucleic    acids as a consequence of the method of any one of embodiments    72-76.-   372. A progeny plant of the plant of embodiment 371.-   373. The progeny plant of embodiment 372, wherein the progeny plant    has reduced expression of the one or more target nucleic acids and    does not comprise the first or second recombinant nucleic acids.-   374. A plant having reduced expression of one or more target nucleic    acids as a consequence of the method of any one of embodiments    182-186 and 360-364.-   375. A progeny plant of the plant of embodiment 374.-   376. The progeny plant of embodiment 375, wherein the progeny plant    has reduced expression of the one or more target nucleic acids and    does not comprise the first recombinant nucleic acid or the one or    more additional recombinant nucleic acids.

We claim:
 1. A method for producing a plant with reduced expression ofone or more target nucleic acids, comprising: (a) providing a plantcomprising a recombinant nucleic acid, wherein the recombinant nucleicacid encodes a recombinant polypeptide comprising a first amino acidsequence comprising a DNA-binding domain and a second amino acidsequence comprising a plant DMS3 polypeptide; and (b) growing the plantunder conditions whereby the recombinant polypeptide encoded by therecombinant nucleic acid is expressed and binds to the one or moretarget nucleic acids, thereby reducing expression of the one or moretarget nucleic acids to produce the plant with reduced expression of theone or more target nucleic acids.
 2. The method of claim 1, wherein theDNA-binding domain comprises a zinc finger domain.
 3. The method ofclaim 1, wherein the DNA-binding domain is selected from the groupconsisting of a TAL effector targeting domain, a helix-turn-helix familyDNA-binding domain, a basic domain, a ribbon-helix-helix domain, a TBPdomain, a barrel dimer domain, a real homology domain, a BAH domain, aSANT domain, a Chromodomain, a Tudor domain, a Bromodomain, a PHDdomain, a WD40 domain, and a MBD domain.
 4. The method of claim 1,wherein the DNA-binding domain comprises a TAL effector targetingdomain.
 5. The method of claim 1, wherein the second amino acid sequencecomprises an amino acid sequence that is at least 70% identical to SEQID NO:
 41. 6. The method of claim 1, wherein the second amino acidsequence comprises an amino acid sequence that is at least 80% identicalto SEQ ID NO:
 41. 7. The method of claim 1, wherein the second aminoacid sequence comprises an amino acid sequence that is at least 90%identical to SEQ ID NO:
 41. 8. The method of claim 1, wherein the one ormore target nucleic acids are endogenous nucleic acids.
 9. The method ofclaim 1, wherein the one or more target nucleic acids are heterologousnucleic acids.
 10. The method of claim 1, wherein expression of the oneor more target nucleic acids is silenced.
 11. The method of claim 1,further comprising: (c) crossing the plant with reduced expression ofthe one or more target nucleic acids to a second plant to produce one ormore F1 plants with reduced expression of the one or more target nucleicacids.
 12. The method of claim 11, further comprising: (d) selectingfrom the one or more F1 plants with reduced expression of the one ormore target nucleic acids an Fl plant that (i) lacks the recombinantnucleic acid, and (ii) has reduced expression of the one or more targetnucleic acids.
 13. A plant cell comprising a recombinant nucleic acidencoding a recombinant polypeptide comprising a first amino acidsequence comprising a DNA-binding domain and a second amino acidsequence comprising a plant DMS3 polypeptide.
 14. The plant cell ofclaim 13, wherein the DNA-binding domain comprises a zinc finger domain.15. The plant cell of claim 13, wherein the DNA-binding domain isselected from the group consisting of a TAL effector targeting domain, ahelix-turn-helix family DNA-binding domain, a basic domain, aribbon-helix-helix domain, a TBP domain, a barrel dimer domain, a realhomology domain, a BAH domain, a SANT domain, a Chromodomain, a Tudordomain, a Bromodomain, a PHD domain, a WD40 domain, and a MBD domain.16. The plant cell of claim 13, wherein the DNA-binding domain comprisesa TAL effector targeting domain.
 17. The plant cell of claim 13, whereinthe second amino acid sequence comprises an amino acid sequence that isat least 70% identical to SEQ ID NO:
 41. 18. The plant cell of claim 13,wherein the second amino acid sequence comprises an amino acid sequencethat is at least 80% identical to SEQ ID NO:
 41. 19. The plant cell ofclaim 13, wherein the second amino acid sequence comprises an amino acidsequence that is at least 90% identical to SEQ ID NO: 41.